format-version: 1.2 date: 13:02:2012 19:03 saved-by: orchard auto-generated-by: OBO-Edit 2.1-rc2 subsetdef: Drugable "Drugable Genome Project" subsetdef: PSI-MI_slim "Subset of PSI-MI" subsetdef: PSI-MOD_slim "subset of protein modifications" synonymtypedef: DeltaMass-label "Label from MS DeltaMass" EXACT synonymtypedef: PSI-MI-alternate "Alternate label curated by PSI-MI" EXACT synonymtypedef: PSI-MI-short "Unique short label curated by PSI-MI" EXACT synonymtypedef: PSI-MOD-alternate "Alternate label curated by PSI-MOD" EXACT synonymtypedef: PSI-MOD-short "Unique short label curated by PSI-MOD" EXACT synonymtypedef: PSI-MS-label "Agreed label from MS community" RELATED synonymtypedef: RESID-alternate "Alternate name from RESID" EXACT synonymtypedef: RESID-misnomer "Misnomer label from RESID" RELATED synonymtypedef: RESID-name "Name from RESID" EXACT synonymtypedef: RESID-systematic "Systematic name from RESID" EXACT synonymtypedef: UniMod-alternate "Alternate name from UniMod" RELATED synonymtypedef: UniMod-description "Description (full_name) from UniMod" RELATED synonymtypedef: UniMod-interim "Interim label from UniMod" RELATED synonymtypedef: UniMod-label "Label (title) from UniMod" RELATED synonymtypedef: UniProt-feature "Protein feature description from UniProtKB" EXACT default-namespace: file:D:/luisa/mergeMIsubsets/MI_MOD_MAP_final.obo remark: Notes: remark: Each of the top level terms in this file is the root term of an independent controlled vocabulary remark: mapping an element of the PSI Molecular Interaction XML schema. remark: The correct use of these vocabularies in the PSI Molecular Interaction XML schema is remark: formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml. remark: The PSI MI schema defines short labels for controlled vocabulary terms remark: short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long. remark: The last accession number used in this file is stored in a separate file, remark: psi-mi.lastac. It MUST be updated when this file is updated. remark: The maintenance of this file is ensured by Sandra Orchard orchard@ebi.ac.uk and Luisa Montecchi Palazzi luisa@ebi.ac.uk remark: coverage: This file collect controlled vocabularies describing different aspects of molecular interactions. remark: publisher: This file is published by the PSI MI working group see http://psidev.info/MI remark: CVversion: 2.5.5 [Term] id: MI:0000 name: molecular interaction namespace: PSI-MI def: "Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "mi" EXACT PSI-MI-short [] [Term] id: MI:0001 name: interaction detection method namespace: PSI-MI def: "Method to determine the interaction." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "interaction detect" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0002 name: participant identification method namespace: PSI-MI def: "Method to determine the molecules involved in the interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "participant detection" EXACT PSI-MI-alternate [] synonym: "participant ident" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0003 name: feature detection method namespace: PSI-MI def: "Method to determine the features of the proteins involved in the interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "feature detection" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0004 name: affinity chromatography technology namespace: PSI-MI def: "This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins." [PMID:7708014] subset: PSI-MI_slim synonym: "affinity chrom" EXACT PSI-MI-short [] synonym: "Affinity purification" EXACT PSI-MI-alternate [] is_a: MI:0091 ! chromatography technology is_a: MI:0400 ! affinity technology [Term] id: MI:0005 name: alanine scanning namespace: PSI-MI def: "This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0810 ! substitution analysis [Term] id: MI:0006 name: anti bait coimmunoprecipitation namespace: PSI-MI def: "A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample." [PMID:7708014] subset: PSI-MI_slim synonym: "anti bait coip" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation [Term] id: MI:0007 name: anti tag coimmunoprecipitation namespace: PSI-MI def: "A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available." [PMID:7708014] subset: PSI-MI_slim synonym: "anti tag coip" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation [Term] id: MI:0008 name: array technology namespace: PSI-MI def: "In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0009 name: bacterial display namespace: PSI-MI def: "The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells." [PMID:10436088, PMID:8248129] subset: PSI-MI_slim is_a: MI:0034 ! display technology is_a: MI:0054 ! fluorescence-activated cell sorting [Term] id: MI:0010 name: beta galactosidase complementation namespace: PSI-MI def: "Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment." [PMID:12042868, PMID:9237989] subset: PSI-MI_slim synonym: "beta galactosidase" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0011 name: beta lactamase complementation namespace: PSI-MI def: "This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications." [PMID:12042868] subset: PSI-MI_slim synonym: "beta lactamase" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0012 name: bioluminescence resonance energy transfer namespace: PSI-MI def: "In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom)." [PMID:9874787, PMID for application instance:10725388] subset: PSI-MI_slim synonym: "BRET" EXACT PSI-MI-alternate [] synonym: "bret" EXACT PSI-MI-short [] synonym: "LRET" EXACT PSI-MI-alternate [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0013 name: biophysical namespace: PSI-MI def: "The application of physical principles and methods to biological experiments." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0014 name: adenylate cyclase complementation namespace: PSI-MI def: "Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene." [PMID:9576956] subset: PSI-MI_slim synonym: "adenylate cyclase" EXACT PSI-MI-short [] synonym: "bacterial two-hybrid" EXACT PSI-MI-alternate [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0016 name: circular dichroism namespace: PSI-MI def: "Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure." [PMID:11578931] subset: PSI-MI_slim synonym: "CD" EXACT PSI-MI-alternate [] synonym: "cd" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0017 name: classical fluorescence spectroscopy namespace: PSI-MI def: "Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage." [PMID:7708014] subset: PSI-MI_slim synonym: "fluorescence spectr" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0018 name: two hybrid namespace: PSI-MI def: "The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator." [PMID:10967325, PMID:12634794, PMID:1946372] subset: PSI-MI_slim synonym: "2 hybrid" EXACT PSI-MI-short [] synonym: "2-hybrid" EXACT PSI-MI-alternate [] synonym: "2H" EXACT PSI-MI-alternate [] synonym: "2h" EXACT PSI-MI-alternate [] synonym: "classical two hybrid" EXACT PSI-MI-alternate [] synonym: "Gal4 transcription regeneration" EXACT PSI-MI-alternate [] synonym: "two-hybrid" EXACT PSI-MI-alternate [] synonym: "Y2H" EXACT [] synonym: "yeast two hybrid" EXACT PSI-MI-alternate [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0019 name: coimmunoprecipitation namespace: PSI-MI def: "In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process." [PMID:7708014] subset: PSI-MI_slim synonym: "co-immunoprecipitation" EXACT PSI-MI-alternate [] synonym: "Co-IP" EXACT PSI-MI-alternate [] synonym: "CoIp" EXACT PSI-MI-alternate [] synonym: "coip" EXACT PSI-MI-short [] synonym: "immunoprecipitation" EXACT PSI-MI-alternate [] is_a: MI:0004 ! affinity chromatography technology [Term] id: MI:0020 name: transmission electron microscopy namespace: PSI-MI def: "During the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell." [PMID:14755292] subset: PSI-MI_slim synonym: "tem" EXACT PSI-MI-short [] is_a: MI:0040 ! electron microscopy [Term] id: MI:0021 name: colocalization by fluorescent probes cloning namespace: PSI-MI def: "Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another.\nOBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein." [PMID:14755292] subset: PSI-MI_slim synonym: "coloc fluoresc probe" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0022 name: colocalization by immunostaining namespace: PSI-MI def: "The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques.\nOBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead." [PMID:14755292] subset: PSI-MI_slim synonym: "coloc immunostaining" EXACT PSI-MI-short [] synonym: "Immunofluorescence Staining" EXACT PSI-MI-alternate [] synonym: "Immunostaining" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0023 name: colocalization/visualisation technologies namespace: PSI-MI def: "Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type.\nOBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection." [PMID:14755292] subset: PSI-MI_slim synonym: "coloc visual technol" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0024 name: confirmational text mining namespace: PSI-MI def: "Text mining is used to support interactions which have been determined by other methods." [PMID:14755292] subset: PSI-MI_slim synonym: "conformational tm" EXACT PSI-MI-short [] is_a: MI:0110 ! text mining [Term] id: MI:0025 name: copurification namespace: PSI-MI def: "Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex.\nOBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401)." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0026 name: correlated mutations namespace: PSI-MI def: "Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces." [PMID:11933068] subset: PSI-MI_slim is_a: MI:0101 ! sequence based prediction is_a: MI:0660 ! feature prediction [Term] id: MI:0027 name: cosedimentation namespace: PSI-MI def: "Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0401 ! biochemical [Term] id: MI:0028 name: cosedimentation in solution namespace: PSI-MI def: "The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed." [PMID:10410796] subset: PSI-MI_slim synonym: "solution sedimentati" EXACT PSI-MI-short [] is_a: MI:0027 ! cosedimentation [Term] id: MI:0029 name: cosedimentation through density gradient namespace: PSI-MI def: "Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant." [PMID:10410796] subset: PSI-MI_slim synonym: "density sedimentatio" EXACT PSI-MI-short [] is_a: MI:0027 ! cosedimentation [Term] id: MI:0030 name: cross-linking study namespace: PSI-MI def: "Analysis of complexes obtained by chemical treatments that promote the formation of covalent bonds among molecules in close proximity." [PMID:14755292] subset: PSI-MI_slim synonym: "crosslink" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical [Term] id: MI:0031 name: protein cross-linking with a bifunctional reagent namespace: PSI-MI def: "A cross-linker is a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. Cross-linkers induce the formation of covalent bonds among proteins that are neighbours. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties." [PMID:10679368, PMID:7708014] subset: PSI-MI_slim synonym: "Label transfer techniques" EXACT PSI-MI-alternate [] synonym: "Photoaffinity labelling" EXACT PSI-MI-alternate [] synonym: "protein crosslink" EXACT PSI-MI-short [] is_a: MI:0030 ! cross-linking study [Term] id: MI:0032 name: de novo protein sequencing by mass spectrometry namespace: PSI-MI def: "The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments." [PMID:10984529] subset: PSI-MI_slim synonym: "de novo protein sequence" EXACT PSI-MI-short [] synonym: "MS/MS" RELATED [] is_a: MI:0093 ! protein sequence identification is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0659 ! experimental feature detection [Term] id: MI:0033 name: deletion analysis namespace: PSI-MI def: "In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0074 ! mutation analysis [Term] id: MI:0034 name: display technology namespace: PSI-MI def: "All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0035 name: docking namespace: PSI-MI def: "Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions." [PMID:9631301, PMID for application instance:11478868] subset: PSI-MI_slim is_a: MI:0105 ! structure based prediction is_a: MI:0577 ! feature prediction from structure [Term] id: MI:0036 name: domain fusion namespace: PSI-MI def: "The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related." [PMID:10573422] subset: PSI-MI_slim synonym: "Rosetta Stone" EXACT PSI-MI-alternate [] is_a: MI:0058 ! genome based prediction is_a: MI:0101 ! sequence based prediction [Term] id: MI:0037 name: domain profile pairs namespace: PSI-MI def: "This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism." [PMID:11473021] subset: PSI-MI_slim is_a: MI:0046 ! experimental knowledge based is_a: MI:0101 ! sequence based prediction is_a: MI:0660 ! feature prediction [Term] id: MI:0038 name: dynamic light scattering namespace: PSI-MI def: "In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated." [PMID:9013660] subset: PSI-MI_slim synonym: "dls" EXACT PSI-MI-short [] is_a: MI:0067 ! light scattering [Term] id: MI:0039 name: edman degradation namespace: PSI-MI def: "In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0433 ! partial identification of protein sequence [Term] id: MI:0040 name: electron microscopy namespace: PSI-MI def: "Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data." [PMID:11785754] subset: PSI-MI_slim synonym: "Electron cryomicroscopy" EXACT PSI-MI-alternate [] synonym: "Electron crystallography" EXACT PSI-MI-alternate [] is_a: MI:0428 ! imaging technique [Term] id: MI:0041 name: electron nuclear double resonance namespace: PSI-MI def: "A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency." [PMID:11817959, PMID:11988476, PMID for application instance:12186859] subset: PSI-MI_slim synonym: "ENDOR" EXACT PSI-MI-alternate [] synonym: "endor" EXACT PSI-MI-short [] is_a: MI:0043 ! electron resonance [Term] id: MI:0042 name: electron paramagnetic resonance namespace: PSI-MI def: "EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment." [PMID:11817959] subset: PSI-MI_slim synonym: "EPR" EXACT PSI-MI-alternate [] synonym: "epr" EXACT PSI-MI-short [] synonym: "ESR" EXACT PSI-MI-alternate [] is_a: MI:0043 ! electron resonance [Term] id: MI:0043 name: electron resonance namespace: PSI-MI def: "A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0013 ! biophysical is_a: MI:0659 ! experimental feature detection [Term] id: MI:0045 name: experimental interaction detection namespace: PSI-MI def: "Methods based on laboratory experiments to determine an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental interac" EXACT PSI-MI-short [] is_a: MI:0001 ! interaction detection method [Term] id: MI:0046 name: experimental knowledge based namespace: PSI-MI def: "Predictive algorithms that rely on the information obtained by experimental results." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental info" EXACT PSI-MI-short [] is_a: MI:0063 ! interaction prediction [Term] id: MI:0047 name: far western blotting namespace: PSI-MI def: "Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody." [PMID:7708014] subset: PSI-MI_slim synonym: "Affinity blotting" EXACT PSI-MI-alternate [] is_a: MI:0892 ! solid phase assay [Term] id: MI:0048 name: filamentous phage display namespace: PSI-MI def: "Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII." [PMID:7682645] subset: PSI-MI_slim synonym: "filamentous phage" EXACT PSI-MI-short [] is_a: MI:0084 ! phage display [Term] id: MI:0049 name: filter binding namespace: PSI-MI def: "A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody." [PMID:7708014] subset: PSI-MI_slim synonym: "dot blot" RELATED [] synonym: "Filter overlay assay" EXACT PSI-MI-alternate [] is_a: MI:0892 ! solid phase assay [Term] id: MI:0050 name: flag tag coimmunoprecipitation namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.\nOBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007)." [PMID:14755292] subset: PSI-MI_slim synonym: "flag tag coip" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0051 name: fluorescence technology namespace: PSI-MI def: "Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescence" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0052 name: fluorescence correlation spectroscopy namespace: PSI-MI def: "FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant." [PMID:10733953] subset: PSI-MI_slim synonym: "FCS" EXACT PSI-MI-alternate [] synonym: "fcs" EXACT PSI-MI-short [] synonym: "fluctuation correlation specctrometry" RELATED [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0053 name: fluorescence polarization spectroscopy namespace: PSI-MI def: "Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled." [PMID:12805227, PMID:7708014] subset: PSI-MI_slim synonym: "Fluorescence anisotropy" EXACT PSI-MI-alternate [] synonym: "FPS" EXACT PSI-MI-alternate [] synonym: "fps" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0054 name: fluorescence-activated cell sorting namespace: PSI-MI def: "Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels." [PMID:11988464] subset: PSI-MI_slim synonym: "FACS" EXACT PSI-MI-alternate [] synonym: "facs" EXACT PSI-MI-short [] synonym: "Flow cytometry" EXACT PSI-MI-alternate [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0055 name: fluorescent resonance energy transfer namespace: PSI-MI def: "FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations." [PMID:11558993] subset: PSI-MI_slim synonym: "FRET" EXACT PSI-MI-alternate [] synonym: "fret" EXACT PSI-MI-short [] synonym: "FRET analysis" EXACT PSI-MI-alternate [] synonym: "RET" EXACT PSI-MI-alternate [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0056 name: full identification by DNA sequencing namespace: PSI-MI def: "Sequencing occurs during the course of the experiment. The DNA to be sequenced is used as template for the in vitro synthesis, by DNA polymerase, of a set of partial replicas, all beginning at the same place, but terminating at different points along the DNA chain. The key to this method is the use of dideoxyribonucleoside triphosphates in which the deoxyribose 3'-OH group present in normal nucleotides is missing; when such a modified nucleotide is incorporated into a DNA chain, it blocks the elongation of the chain. To determine the full sequence, the four different chain-terminating dideoxyribonucleosides are used in competition with an excess of deoxyribonucleosides in separate DNA synthesis reactions on the same DNA template. When the products of these four reactions are analysed by electrophoresis in four parallel lanes of a denaturing polyacrylamide gel, the DNA sequence can be derived. Every lane displays a family of DNA fragments of different lengths, reflecting the different sites at which a specific residue occurs in the original DNA." [PMID:14755292] subset: PSI-MI_slim synonym: "full dna sequence" EXACT PSI-MI-short [] is_a: MI:0078 ! nucleotide sequence identification is_a: MI:0659 ! experimental feature detection [Term] id: MI:0057 name: gene neighbourhood namespace: PSI-MI def: "Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred." [PMID:9787636] subset: PSI-MI_slim is_a: MI:0058 ! genome based prediction [Term] id: MI:0058 name: genome based prediction namespace: PSI-MI def: "Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes." [PMID:14755292] subset: PSI-MI_slim synonym: "genome prediction" EXACT PSI-MI-short [] is_a: MI:0063 ! interaction prediction [Term] id: MI:0059 name: gst pull down namespace: PSI-MI def: "The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody.\nOBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096)." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0060 name: ha tag coimmunoprecipitation namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.\nOBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007)." [PMID:14755292] subset: PSI-MI_slim synonym: "ha tag coip" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0061 name: his pull down namespace: PSI-MI def: "The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin.\nOBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096)." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0062 name: his tag coimmunoprecipitation namespace: PSI-MI def: "The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.\nOBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007)." [PMID:14755292] subset: PSI-MI_slim synonym: "his tag coip" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0063 name: interaction prediction namespace: PSI-MI def: "Computational methods to predict an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "in silico methods" EXACT PSI-MI-alternate [] synonym: "predicted interac" EXACT PSI-MI-short [] is_a: MI:0001 ! interaction detection method [Term] id: MI:0064 name: interologs mapping namespace: PSI-MI def: "Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties." [PMID:11731503] subset: PSI-MI_slim synonym: "Homology based interaction prediction" EXACT PSI-MI-alternate [] is_a: MI:0046 ! experimental knowledge based is_a: MI:0101 ! sequence based prediction [Term] id: MI:0065 name: isothermal titration calorimetry namespace: PSI-MI def: "Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS." [PMID:11785756] subset: PSI-MI_slim synonym: "ITC" EXACT PSI-MI-alternate [] synonym: "itc" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0066 name: lambda phage display namespace: PSI-MI def: "Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid." [PMID:7682645] subset: PSI-MI_slim synonym: "lambda phage" EXACT PSI-MI-short [] is_a: MI:0084 ! phage display [Term] id: MI:0067 name: light scattering namespace: PSI-MI def: "Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam." [PMID:9013660] subset: PSI-MI_slim is_a: MI:0013 ! biophysical [Term] id: MI:0068 name: mass detection of residue modification namespace: PSI-MI def: "Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies." [PMID:11395414, PMID for application instance:11875433] subset: PSI-MI_slim synonym: "modified residue ms" EXACT PSI-MI-short [] is_a: MI:0659 ! experimental feature detection [Term] id: MI:0069 name: mass spectrometry studies of complexes namespace: PSI-MI def: "Mass spectrometric approaches to the study of protein in complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation." [PMID:12504676, PMID for application instance:12057199] subset: PSI-MI_slim synonym: "ms of complexes" EXACT PSI-MI-short [] is_a: MI:0943 ! detection by mass spectrometry [Term] id: MI:0070 name: mobility shift namespace: PSI-MI def: "Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection [Term] id: MI:0071 name: molecular sieving namespace: PSI-MI def: "In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction." [PMID:7708014] subset: PSI-MI_slim synonym: "Gel Filtration" EXACT PSI-MI-alternate [] synonym: "Siezing column" EXACT PSI-MI-alternate [] synonym: "Size Exclusion Chromatography" EXACT PSI-MI-alternate [] is_a: MI:0013 ! biophysical is_a: MI:0091 ! chromatography technology [Term] id: MI:0072 name: monoclonal antibody western blot namespace: PSI-MI def: "Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology." [PMID:14755292] subset: PSI-MI_slim synonym: "monoclonal western" EXACT PSI-MI-short [] is_a: MI:0113 ! western blot [Term] id: MI:0073 name: mrna display namespace: PSI-MI def: "This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins." [PMID:11551470] subset: PSI-MI_slim is_a: MI:0034 ! display technology [Term] id: MI:0074 name: mutation analysis namespace: PSI-MI def: "Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection [Term] id: MI:0075 name: myc tag coimmunoprecipitation namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.\nOBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007)." [PMID:14755292] subset: PSI-MI_slim synonym: "myc tag coip " EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0076 name: neural network on interface properties namespace: PSI-MI def: "Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface." [PMID:11455607, PMID:11874449] subset: PSI-MI_slim synonym: "interface predictor" EXACT PSI-MI-short [] is_a: MI:0577 ! feature prediction from structure [Term] id: MI:0077 name: nuclear magnetic resonance namespace: PSI-MI def: "Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions." [PMID:12120505, PMID for application instance:12062432] subset: PSI-MI_slim synonym: "NMR" EXACT PSI-MI-alternate [] synonym: "nmr" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical is_a: MI:0659 ! experimental feature detection [Term] id: MI:0078 name: nucleotide sequence identification namespace: PSI-MI def: "Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones." [PMID:14755292] subset: PSI-MI_slim synonym: "nucleotide sequence" EXACT PSI-MI-short [] synonym: "sequence cloning" EXACT PSI-MI-alternate [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0079 name: other biochemical technologies namespace: PSI-MI def: "Experimental methods that could not be assigned to the other large group of technologies.\nOBSOLETE use biochemical (MI:0401) instead." [PMID:14755292] subset: PSI-MI_slim synonym: "other biochemic tech" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0080 name: partial dna sequence identification by hybridization namespace: PSI-MI def: "Genes are recognised by hybridization of a probe with a fragment of the gene sequence." [PMID:14755292] subset: PSI-MI_slim synonym: "partial dna sequence" EXACT PSI-MI-short [] is_a: MI:0078 ! nucleotide sequence identification [Term] id: MI:0081 name: peptide array namespace: PSI-MI def: "The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support." [PMID:11167074] subset: PSI-MI_slim is_a: MI:0008 ! array technology [Term] id: MI:0082 name: peptide massfingerprinting namespace: PSI-MI def: "This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer." [PMID:10967324, PMID:11752590, PMID for application instance:11805826] subset: PSI-MI_slim synonym: "fingerprinting" EXACT PSI-MI-short [] is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0433 ! partial identification of protein sequence [Term] id: MI:0083 name: peptide synthesis namespace: PSI-MI def: "When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0093 ! protein sequence identification [Term] id: MI:0084 name: phage display namespace: PSI-MI def: "Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7)." [PMID:10975452, PMID:7708014] subset: PSI-MI_slim is_a: MI:0034 ! display technology [Term] id: MI:0085 name: phylogenetic profile namespace: PSI-MI def: "The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified." [PMID:10200254] subset: PSI-MI_slim is_a: MI:0058 ! genome based prediction [Term] id: MI:0086 name: polyclonal antibody western blot namespace: PSI-MI def: "Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest." [PMID:14755292] subset: PSI-MI_slim synonym: "polyclonal western" EXACT PSI-MI-short [] is_a: MI:0113 ! western blot [Term] id: MI:0087 name: predictive text mining namespace: PSI-MI def: "Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them." [PMID:11791231] subset: PSI-MI_slim synonym: "predictive tm" EXACT PSI-MI-short [] is_a: MI:0110 ! text mining [Term] id: MI:0088 name: primer specific pcr namespace: PSI-MI def: "Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0080 ! partial dna sequence identification by hybridization [Term] id: MI:0089 name: protein array namespace: PSI-MI def: "The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait." [PMID:10976071, PMID:12067604] subset: PSI-MI_slim is_a: MI:0008 ! array technology [Term] id: MI:0090 name: protein complementation assay namespace: PSI-MI def: "In the protein-fragment complementation assay, the proteins of interest (\"Bait\" and \"Prey\") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the \"reporter\") and are expressed in vivo, Interaction between the \"bait\" and the \"prey\" proteins brings the fragments of the \"reporter\" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode." [PMID:11495741] subset: PSI-MI_slim synonym: "complementation" EXACT PSI-MI-short [] synonym: "PCA" EXACT PSI-MI-alternate [] is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0091 name: chromatography technology namespace: PSI-MI def: "Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC)." [PMID:14755292] subset: PSI-MI_slim synonym: "chromatography" EXACT PSI-MI-short [] synonym: "column chromatography" EXACT PSI-MI-alternate [] is_a: MI:0401 ! biochemical [Term] id: MI:0092 name: protein in situ array namespace: PSI-MI def: "Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a double HexaHis-tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised." [PMID:11470888] subset: PSI-MI_slim synonym: "PISA" EXACT PSI-MI-alternate [] synonym: "pisa" EXACT PSI-MI-short [] is_a: MI:0089 ! protein array [Term] id: MI:0093 name: protein sequence identification namespace: PSI-MI def: "Single amino acid identification along a protein sequence." [PMID:14755292] subset: PSI-MI_slim synonym: "protein sequence" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0094 name: protein staining namespace: PSI-MI def: "A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation." [PMID:12015990] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection [Term] id: MI:0095 name: proteinchip(r) on a surface-enhanced laser desorption/ionization namespace: PSI-MI def: "ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry." [PMID:11827829] subset: PSI-MI_slim synonym: "seldi chip" EXACT PSI-MI-short [] synonym: "SELDI ProteinChip" EXACT PSI-MI-alternate [] is_a: MI:0089 ! protein array [Term] id: MI:0096 name: pull down namespace: PSI-MI def: "A specific affinity chromatography method where a molecule of interest (bait) is expressed as a fusion to an affinity tag (GST, HIS tag and others) and binds to a support that has affinity for the tag. The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0004 ! affinity chromatography technology [Term] id: MI:0097 name: reverse ras recruitment system namespace: PSI-MI def: "In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation." [PMID:11160938] subset: PSI-MI_slim synonym: "reverse RRS" EXACT PSI-MI-alternate [] synonym: "reverse rrs" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0098 name: ribosome display namespace: PSI-MI def: "This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties." [PMID:11551470, PMID for application instance:12167034] subset: PSI-MI_slim is_a: MI:0034 ! display technology [Term] id: MI:0099 name: scintillation proximity assay namespace: PSI-MI def: "SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present." [PMID:3866247] subset: PSI-MI_slim synonym: "RIA Radio Immuno Assay" EXACT PSI-MI-alternate [] synonym: "SPA" EXACT PSI-MI-alternate [] synonym: "spa" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0100 name: sequence based phylogenetic profile namespace: PSI-MI def: "Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible protein pairs. The covariation of the distance matrices reveals interacting protein pairs." [PMID:11707606] subset: PSI-MI_slim synonym: "sequence phylogeny" EXACT PSI-MI-short [] is_a: MI:0058 ! genome based prediction is_a: MI:0101 ! sequence based prediction [Term] id: MI:0101 name: sequence based prediction namespace: PSI-MI def: "Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs." [PMID:14755292] subset: PSI-MI_slim synonym: "predict from sequenc" EXACT PSI-MI-short [] is_a: MI:0063 ! interaction prediction [Term] id: MI:0102 name: sequence tag identification namespace: PSI-MI def: "This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases." [PMID:10967324, PMID:11752590, PMID for application instance:11805837] subset: PSI-MI_slim synonym: "MS/MS" RELATED [] synonym: "sequence tag" EXACT PSI-MI-short [] is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0433 ! partial identification of protein sequence [Term] id: MI:0103 name: southern blot namespace: PSI-MI def: "A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0080 ! partial dna sequence identification by hybridization [Term] id: MI:0104 name: static light scattering namespace: PSI-MI def: "In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions." [PMID:9013660] subset: PSI-MI_slim synonym: "sls" EXACT PSI-MI-short [] is_a: MI:0067 ! light scattering [Term] id: MI:0105 name: structure based prediction namespace: PSI-MI def: "Methods based on 3D structure information." [PMID:14755292] subset: PSI-MI_slim synonym: "predict from struct" EXACT PSI-MI-short [] is_a: MI:0063 ! interaction prediction [Term] id: MI:0106 name: surface patches namespace: PSI-MI def: "Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions." [PMID:9299343] subset: PSI-MI_slim is_a: MI:0577 ! feature prediction from structure [Term] id: MI:0107 name: surface plasmon resonance namespace: PSI-MI def: "This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation." [PMID:11896282, PMID:12120258, PMID:16338355] subset: PSI-MI_slim synonym: "BIAcore(r)" EXACT PSI-MI-alternate [] synonym: "Optical biosensor" EXACT PSI-MI-alternate [] synonym: "spr" EXACT PSI-MI-short [] is_a: MI:0659 ! experimental feature detection is_a: MI:0968 ! biosensor [Term] id: MI:0108 name: t7 phage display namespace: PSI-MI def: "T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved." [PMID:14755292] comment: Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1. subset: PSI-MI_slim synonym: "t7 phage" EXACT PSI-MI-short [] is_a: MI:0084 ! phage display [Term] id: MI:0109 name: tap tag coimmunoprecipitation namespace: PSI-MI def: "The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag).\nOBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676)." [PMID:10504710] subset: PSI-MI_slim synonym: "tap tag coip" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0110 name: text mining namespace: PSI-MI def: "Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0046 ! experimental knowledge based [Term] id: MI:0111 name: dihydrofolate reductase reconstruction namespace: PSI-MI def: "The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled." [PMID:10318894] subset: PSI-MI_slim synonym: "dhfr reconstruction" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0112 name: ubiquitin reconstruction namespace: PSI-MI def: "In this method the two proteins, whose interaction is under investigation, (in this case mostly membrane proteins) are fused to an terminal fragment (Nub) and to a C-terminal fragment of ubiquitin (Cub). The two fragments do not associate to form a functional ubiquitin unless the two fused membrane proteins form a complex. The association is monitored by an ingenious trick. The C-term fragment of ubiquitin is expressed as a fusion to a transcription factor that being linked to a membrane protein cannot perform its function unless it is released form the ubiquitin fusion by a specific protease. This achieved through the activity of UBP (an ubiquitin specific protease) that cleaves off the reporter protein only when a functional ubiquitin is reconstituted." [PMID:9560251] subset: PSI-MI_slim synonym: "ub reconstruction" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0113 name: western blot namespace: PSI-MI def: "Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane." [PMID:14755292] subset: PSI-MI_slim synonym: "Immuno blot" EXACT PSI-MI-alternate [] is_a: MI:0421 ! identification by antibody is_a: MI:0659 ! experimental feature detection [Term] id: MI:0114 name: x-ray crystallography namespace: PSI-MI def: "Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallisation conditions." [PMID:14755292] subset: PSI-MI_slim synonym: "X-ray" EXACT PSI-MI-alternate [] synonym: "x-ray diffraction" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical is_a: MI:0659 ! experimental feature detection [Term] id: MI:0115 name: yeast display namespace: PSI-MI def: "The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties." [PMID:9181578] subset: PSI-MI_slim is_a: MI:0034 ! display technology is_a: MI:0054 ! fluorescence-activated cell sorting [Term] id: MI:0116 name: feature type namespace: PSI-MI def: "Property of a subsequence that may interfere with the binding of a molecule." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0117 name: binding-associated region namespace: PSI-MI def: "A region of a molecule identified as being involved in an interaction. This may or may not be a region of the protein in direct contact with the interacting partner." [PMID:14755292] subset: PSI-MI_slim synonym: "binding region" EXACT PSI-MI-short [] synonym: "binding site" BROAD [] is_a: MI:0252 ! biological feature [Term] id: MI:0118 name: mutation namespace: PSI-MI def: "Sequence variation due to insertion, deletion or substitution event." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0252 ! biological feature [Term] id: MI:0119 name: mutation decreasing interaction namespace: PSI-MI def: "Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction)." [PMID:14755292] subset: PSI-MI_slim synonym: "hotspot" EXACT PSI-MI-alternate [] synonym: "mutation decreasing" EXACT PSI-MI-short [] is_a: MI:0118 ! mutation [Term] id: MI:0120 name: post translation modification namespace: PSI-MI def: "Residue covalent modifications occurring in the specific protein form involved in an interaction.\nOBSOLETE remap to MOD:00000." [PMID:14755292] synonym: "ptm" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0121 name: acetylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00394." [PMID:11125103] is_obsolete: true [Term] id: MI:0122 name: n-acetyl-alanine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00050." [PMID:11125103, RESID:AA0041] synonym: "(S)-2-(acetylamino)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[A:ac]" EXACT PSI-MI-alternate [] synonym: "AAC" EXACT PSI-MI-alternate [] synonym: "acetylalanine" EXACT PSI-MI-alternate [] synonym: "acetylalanine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-alanine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0123 name: n2-acetyl-arginine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00359." [PMID:11125103, RESID:AA0354] synonym: "[R:ac]" EXACT PSI-MI-alternate [] synonym: "acetylarginine" EXACT PSI-MI-alternate [] synonym: "acetylarginine" EXACT PSI-MI-short [] synonym: "alpha-acetylamino-delta-guanidinovaleric acid" EXACT PSI-MI-alternate [] synonym: "N2-acetyl-L-arginine" EXACT PSI-MI-alternate [] synonym: "RAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0124 name: n-acetyl-asparagine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00780." [PMID:11125103] synonym: "[N:ac]" EXACT PSI-MI-alternate [] synonym: "acetylasparagine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-asparagine" EXACT PSI-MI-alternate [] synonym: "NAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0125 name: n-acetyl-aspartic acid namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00051." [PMID:11125103, RESID:AA0042] synonym: "(S)-2-(acetylamino)butanedioic acid" EXACT PSI-MI-alternate [] synonym: "[D:ac]" EXACT PSI-MI-alternate [] synonym: "acetylaspartate" EXACT PSI-MI-short [] synonym: "acetylaspartic acid" EXACT PSI-MI-alternate [] synonym: "DAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-aspartic acid" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0126 name: n-acetyl-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00052." [PMID:11125103, RESID:AA0043] synonym: "(R)-2-acetylamino-3-sulfanylpropanoic acid" EXACT PSI-MI-alternate [] synonym: "2-acetylamino-3-mercaptopropanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:ac]" EXACT PSI-MI-alternate [] synonym: "acetylcysteine" EXACT PSI-MI-short [] synonym: "CAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-cysteine" EXACT PSI-MI-alternate [] synonym: "N-acetylcysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0127 name: n-acetyl-glutamine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00054." [PMID:11125103, RESID:AA0045] synonym: "(S)-2-acetylamino-5-pentanediamic acid" EXACT PSI-MI-alternate [] synonym: "[Q:ac]" EXACT PSI-MI-alternate [] synonym: "acetylglutamine" EXACT PSI-MI-alternate [] synonym: "acetylglutamine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-glutamine" EXACT PSI-MI-alternate [] synonym: "QAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0128 name: n-acetyl-glutamic acid namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00053." [PMID:11125103, RESID:AA0044] synonym: "(S)-2-(acetylamino)pentanedioic acid" EXACT PSI-MI-alternate [] synonym: "[E:ac]" EXACT PSI-MI-alternate [] synonym: "acetylglutamate" EXACT PSI-MI-short [] synonym: "acetylglutamic acid" EXACT PSI-MI-alternate [] synonym: "EAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-glutamic acid" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0129 name: n-acetylglycine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00055." [PMID:11125103, RESID:AA0046] synonym: "2-(acetylamino)ethanoic acid" EXACT PSI-MI-alternate [] synonym: "[G:ac]" EXACT PSI-MI-alternate [] synonym: "aceturic acid" EXACT PSI-MI-alternate [] synonym: "acetylglycine" EXACT PSI-MI-short [] synonym: "GAC" EXACT PSI-MI-alternate [] synonym: "N-acetylglycine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0130 name: n-acetyl-histidine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00781." [PMID:11125103] synonym: "[H:ac]" EXACT PSI-MI-alternate [] synonym: "acetylhistidine" EXACT PSI-MI-short [] synonym: "HAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-histidine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0131 name: n-acetyl-isoleucine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00056." [PMID:11125103, RESID:AA0047] synonym: "(2S,3S)-2-acetylamino-3-methylpentanoic acid" EXACT PSI-MI-alternate [] synonym: "[I:ac]" EXACT PSI-MI-alternate [] synonym: "acetylisoleucine" EXACT PSI-MI-alternate [] synonym: "acetylisoleucine" EXACT PSI-MI-short [] synonym: "IAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-isoleucine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0132 name: n-acetyl-leucine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00782." [PMID:11125103] synonym: "[L:ac]" EXACT PSI-MI-alternate [] synonym: "acetylleucine" EXACT PSI-MI-short [] synonym: "LAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-leucine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0133 name: n2-acetyl-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00057." [PMID:11125103, RESID:AA0048] synonym: "(S)-2-acetylamino-6-aminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:ac]" EXACT PSI-MI-alternate [] synonym: "KAC" EXACT PSI-MI-alternate [] synonym: "N2-acetyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "N2-acetyllysine" EXACT PSI-MI-alternate [] synonym: "n2-acetyllysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0134 name: n6-acetyl-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00064." [PMID:11125103, RESID:AA0055] synonym: "(S)-2-amino-6-(acetylamino)hexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:N6ac]" EXACT PSI-MI-alternate [] synonym: "epsilon-acetyllysine" EXACT PSI-MI-alternate [] synonym: "KA6" EXACT PSI-MI-alternate [] synonym: "N(zeta)-acetyllysine" EXACT PSI-MI-alternate [] synonym: "N6-acetyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "n6-acetyllysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0135 name: n-acetyl-methionine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00058." [PMID:11125103, RESID:AA0049] synonym: "(S)-2-acetylamino-4-(methylsulfanyl)butanoic acid" EXACT PSI-MI-alternate [] synonym: "2-acetylamino-4-(methylthio)butanoic acid" EXACT PSI-MI-alternate [] synonym: "[M:ac]" EXACT PSI-MI-alternate [] synonym: "acetylmethionine" EXACT PSI-MI-alternate [] synonym: "acetylmethionine" EXACT PSI-MI-short [] synonym: "MAC" EXACT PSI-MI-alternate [] synonym: "methionamine" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-methionine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0136 name: n-acetyl-phenylalanine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00784." [PMID:11125103] synonym: "[F:ac]" EXACT PSI-MI-alternate [] synonym: "acetylphenylalanine" EXACT PSI-MI-short [] synonym: "FAC" EXACT PSI-MI-alternate [] synonym: "N-acetyl-L-phenylalanine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0137 name: n-acetyl-proline namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00059." [PMID:11125103, RESID:AA0050] synonym: "(2S)-1-acetyl-2-pyrrolidinecarboxylic acid" EXACT PSI-MI-alternate [] synonym: "[P:ac]" EXACT PSI-MI-alternate [] synonym: "acetylproline" EXACT PSI-MI-alternate [] synonym: "acetylproline" EXACT PSI-MI-short [] synonym: "N-acetyl-L-proline" EXACT PSI-MI-alternate [] synonym: "PAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0138 name: n-acetyl-serine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00060." [PMID:11125103, RESID:AA0051] synonym: "(S)-2-acetylamino-3-hydroxypropanoic acid" EXACT PSI-MI-alternate [] synonym: "[S:ac]" EXACT PSI-MI-alternate [] synonym: "acetylserine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-serine" EXACT PSI-MI-alternate [] synonym: "N-acetylserine" EXACT PSI-MI-alternate [] synonym: "SAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0139 name: n-acetyl-threonine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00061." [PMID:11125103, RESID:AA0052] synonym: "(2S,3R)-2-acetylamino-3-hydroxybutanoic acid" EXACT PSI-MI-alternate [] synonym: "[T:ac]" EXACT PSI-MI-alternate [] synonym: "acetylthreonine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-threonine" EXACT PSI-MI-alternate [] synonym: "N-acetylthreonine" EXACT PSI-MI-alternate [] synonym: "TAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0140 name: n-acetyl-tryptophan namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00785." [PMID:11125103] synonym: "[W:ac]" EXACT PSI-MI-alternate [] synonym: "acetyltryptophan" EXACT PSI-MI-short [] synonym: "N-acetyl-L-tryptophan" EXACT PSI-MI-alternate [] synonym: "WAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0141 name: n-acetyl-tyrosine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00062." [PMID:11125103, RESID:AA0053] synonym: "(S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[Y:ac]" EXACT PSI-MI-alternate [] synonym: "acetyltyrosine" EXACT PSI-MI-short [] synonym: "N-acetyl-L-tyrosine" EXACT PSI-MI-alternate [] synonym: "N-acetyltyrosine" EXACT PSI-MI-alternate [] synonym: "YAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0142 name: n-acetyl-valine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00063." [PMID:11125103, RESID:AA0054] synonym: "(S)-2-acetylamino-3-methylbutanoic acid" EXACT PSI-MI-alternate [] synonym: "[V:ac]" EXACT PSI-MI-alternate [] synonym: "acetylvaline" EXACT PSI-MI-short [] synonym: "N-acetyl-L-valine" EXACT PSI-MI-alternate [] synonym: "N-acetylvaline" EXACT PSI-MI-alternate [] synonym: "VAC" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0143 name: amidated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00674." [PMID:11125103] is_obsolete: true [Term] id: MI:0144 name: alanine amide namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00090." [PMID:14755292] synonym: "(S)-2-aminopropanamide" EXACT PSI-MI-alternate [] synonym: "[A:am]" EXACT PSI-MI-alternate [] synonym: "AAM" EXACT PSI-MI-alternate [] synonym: "alaninamide" EXACT PSI-MI-alternate [] synonym: "alanineamide" EXACT PSI-MI-short [] synonym: "L-alanine amide" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0145 name: arginine amide namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00091." [PMID:11125103, RESID:AA0082] synonym: "(S)-2-amino-5-guanidinopentanamide" EXACT PSI-MI-alternate [] synonym: "[R:am]" EXACT PSI-MI-alternate [] synonym: "argininamide" EXACT PSI-MI-alternate [] synonym: "arginineamide" EXACT PSI-MI-short [] synonym: "L-arginine amide" EXACT PSI-MI-alternate [] synonym: "RAM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0146 name: formylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00493." [PMID:11125103] is_obsolete: true [Term] id: MI:0147 name: n-formyl-methionine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00030." [PMID:11125103, RESID:AA0021] synonym: "(S)-2-formylamino-4-(methylsulfanyl)butanoic acid" EXACT PSI-MI-alternate [] synonym: "2-formylamino-4-(methylthio)butanoic acid" EXACT PSI-MI-alternate [] synonym: "[M:form]" EXACT PSI-MI-alternate [] synonym: "formylmethionine" EXACT PSI-MI-short [] synonym: "MFM" EXACT PSI-MI-alternate [] synonym: "N-formyl-L-methionine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0148 name: hydroxylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00428." [PMID:11125103] is_obsolete: true [Term] id: MI:0149 name: 4-hydroxy-proline namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00039." [PMID:11125103, RESID:AA0030] synonym: "4-hydroxy-L-proline" EXACT PSI-MI-alternate [] synonym: "4hydroxyproline" EXACT PSI-MI-short [] synonym: "[P:hy_g]" EXACT PSI-MI-alternate [] synonym: "HYP" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0150 name: lipid modification namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:01155." [PMID:11125103] is_obsolete: true [Term] id: MI:0151 name: s-farnesyl-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00111." [PMID:11125103, RESID:AA0102] synonym: "(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:farn]" EXACT PSI-MI-alternate [] synonym: "CFN" EXACT PSI-MI-alternate [] synonym: "farnesylcysteine" EXACT PSI-MI-short [] synonym: "S-farnesyl-L-cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0152 name: s-geranylgeranyl-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00113." [PMID:11125103, RESID:AA0104] synonym: "(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:ger]" EXACT PSI-MI-alternate [] synonym: "CGR" EXACT PSI-MI-alternate [] synonym: "geranylgeranylcys" EXACT PSI-MI-short [] synonym: "S-geranylgeranyl-L-cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0153 name: n-palmitoyl-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00069." [PMID:11125103, RESID:AA0060] synonym: "(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid" EXACT PSI-MI-alternate [] synonym: "2-hexadecanoylamino-3-mercaptopropanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:palm_n]" EXACT PSI-MI-alternate [] synonym: "CPN" EXACT PSI-MI-alternate [] synonym: "N-(1-oxahexadecyl)-L-cysteine" EXACT PSI-MI-alternate [] synonym: "N-palmitoyl-L-cysteine" EXACT PSI-MI-alternate [] synonym: "n-palmitoylcysteine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0154 name: s-palmitoyl-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00115." [PMID:11125103, RESID:AA0106] synonym: "(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(hexadecanoylthio)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:palm_s]" EXACT PSI-MI-alternate [] synonym: "CPS" EXACT PSI-MI-alternate [] synonym: "cysteine hexadecanoate thioester" EXACT PSI-MI-alternate [] synonym: "cysteine palmitate thioester" EXACT PSI-MI-alternate [] synonym: "S-palmitoyl-L-cysteine" EXACT PSI-MI-alternate [] synonym: "s-palmitoylcysteine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0155 name: n-myristoyl-glycine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00068." [PMID:11125103, RESID:AA0059] synonym: "[G:myr]" EXACT PSI-MI-alternate [] synonym: "GMY" EXACT PSI-MI-alternate [] synonym: "myristoylglycine" EXACT PSI-MI-short [] synonym: "N-myristoyl-glycine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0156 name: n6-myristoyl-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00087." [PMID:11125103, RESID:AA0078] synonym: "(S)-2-amino-6-(tetradecanoylamino)hexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:myr]" EXACT PSI-MI-alternate [] synonym: "epsilon-myristoyllysine" EXACT PSI-MI-alternate [] synonym: "KMY" EXACT PSI-MI-alternate [] synonym: "myristoyllysine" EXACT PSI-MI-short [] synonym: "N(zeta)-myristoyllysine" EXACT PSI-MI-alternate [] synonym: "N6-(1-oxotetradecyl)-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-myristoyl-L-lysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0157 name: methylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00427." [PMID:11125103] is_obsolete: true [Term] id: MI:0158 name: n-methyl-alanine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00070." [PMID:11125103, RESID:AA0061] synonym: "(S)-2-methylaminopropanoic acid" EXACT PSI-MI-alternate [] synonym: "[A:meth_n]" EXACT PSI-MI-alternate [] synonym: "AMT" EXACT PSI-MI-alternate [] synonym: "methylalanine" EXACT PSI-MI-short [] synonym: "N-methyl-L-alanine" EXACT PSI-MI-alternate [] synonym: "N-methylalanine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0159 name: n,n,n-trimethyl-alanine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00071." [PMID:11125103, RESID:AA0062] synonym: "(S)-1-carboxy-N,N,N-trimethylethanaminium" EXACT PSI-MI-alternate [] synonym: "(S)-2-(trimethylammonio)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[A:meth_n3]" EXACT PSI-MI-alternate [] synonym: "AM3" EXACT PSI-MI-alternate [] synonym: "N,N,N-trimethyl-L-alanine" EXACT PSI-MI-alternate [] synonym: "trimethylalanine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0160 name: omega-n,omega-n-dimethyl-arginine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00077." [PMID:11125103, RESID:AA0068] synonym: "(S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid" EXACT PSI-MI-alternate [] synonym: "[R:meth_n7]" EXACT PSI-MI-alternate [] synonym: "asymmetric dimethylarginine" EXACT PSI-MI-alternate [] synonym: "dimethylarginine" EXACT PSI-MI-short [] synonym: "NG,NG-dimethylarginine" EXACT PSI-MI-alternate [] synonym: "omega-N,omega-N-dimethyl-L-arginine" EXACT PSI-MI-alternate [] synonym: "RM2" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0161 name: beta-methylthioaspartic acid namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00237." [PMID:11125103, RESID:AA0232] synonym: "(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid" EXACT PSI-MI-alternate [] synonym: "3-carboxy-S-methyl-cysteine" EXACT PSI-MI-alternate [] synonym: "3-methylthio-aspartic acid" EXACT PSI-MI-alternate [] synonym: "[D:meth_b]" EXACT PSI-MI-alternate [] synonym: "beta-methylthio-aspartic acid" EXACT PSI-MI-alternate [] synonym: "DM2" EXACT PSI-MI-alternate [] synonym: "L-beta-methylthioaspartic acid" EXACT PSI-MI-alternate [] synonym: "methylthioaspartate" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0162 name: n5-methyl-glutamine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00080." [PMID:11125103, RESID:AA0071] synonym: "(S)-2-amino-N5-methylpentanediamic acid" EXACT PSI-MI-alternate [] synonym: "[Q:meth_n5]" EXACT PSI-MI-alternate [] synonym: "gamma-methylglutamine" EXACT PSI-MI-alternate [] synonym: "methylglutamine" EXACT PSI-MI-short [] synonym: "N(delta)-methylglutamine" EXACT PSI-MI-alternate [] synonym: "N-methylglutamine" EXACT PSI-MI-alternate [] synonym: "N5-methyl-L-glutamine" EXACT PSI-MI-alternate [] synonym: "QM5" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0163 name: glutamic acid 5-methyl ester namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00081." [PMID:11125103, RESID:AA0072] synonym: "(S)-2-aminopentanedioic acid 5-methyl ester" EXACT PSI-MI-alternate [] synonym: "5-methyl-L-glutamate" EXACT PSI-MI-alternate [] synonym: "[E:meth_o5]" EXACT PSI-MI-alternate [] synonym: "EM5" EXACT PSI-MI-alternate [] synonym: "glutamatemethylester" EXACT PSI-MI-short [] synonym: "glutamic acid gamma-methyl ester" EXACT PSI-MI-alternate [] synonym: "L-glutamic acid 5-methyl ester" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0164 name: 3'-methyl-histidine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00082." [PMID:11125103, RESID:AA0073] synonym: "(S)-2-amino-3-(3-methyl-3H-imidazol-4-yl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "1-methylhistidine [misnomer]" EXACT PSI-MI-alternate [] synonym: "3'-methyl-L-histidine" EXACT PSI-MI-alternate [] synonym: "[H:meth_n4]" EXACT PSI-MI-alternate [] synonym: "methylhistidine" EXACT PSI-MI-short [] synonym: "MHS" EXACT PSI-MI-alternate [] synonym: "N(delta)-methylhistidine" EXACT PSI-MI-alternate [] synonym: "pi-methylhistidine" EXACT PSI-MI-alternate [] synonym: "pros-methylhistidine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0165 name: n6-methyl-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00085." [PMID:11125103] synonym: "(S)-2-amino-6-methylaminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:meth_1]" EXACT PSI-MI-alternate [] synonym: "epsilon-methyllysine" EXACT PSI-MI-alternate [] synonym: "methyllysine" EXACT PSI-MI-short [] synonym: "MLZ" EXACT PSI-MI-alternate [] synonym: "N(zeta)-methyllysine" EXACT PSI-MI-alternate [] synonym: "N6-methyl-L-lysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0166 name: n6,n6-dimethyl-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00084." [PMID:11125103, RESID:AA0075] synonym: "(S)-2-amino-6-dimethylaminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:meth_2]" EXACT PSI-MI-alternate [] synonym: "dimethyllysine" EXACT PSI-MI-short [] synonym: "epsilon-dimethyllysine" EXACT PSI-MI-alternate [] synonym: "lysine derivative Lys(y)" EXACT PSI-MI-alternate [] synonym: "MLY" EXACT PSI-MI-alternate [] synonym: "N(zeta)-dimethyllysine" EXACT PSI-MI-alternate [] synonym: "N6,N6-dimethyl-L-lysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0167 name: n6,n6,n6-trimethyl-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00083." [PMID:11125103, RESID:AA0074] synonym: "(S)-2-amino-6-(trimethylammonio)hexanoic acid" EXACT PSI-MI-alternate [] synonym: "(S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium" EXACT PSI-MI-alternate [] synonym: "[K:meth_3]" EXACT PSI-MI-alternate [] synonym: "epsilon-trimethyllysine" EXACT PSI-MI-alternate [] synonym: "M3L" EXACT PSI-MI-alternate [] synonym: "N(zeta)-trimethyllysine" EXACT PSI-MI-alternate [] synonym: "N6,N6,N6-trimethyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "trimethyllysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0168 name: n-methyl-methionine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00073." [PMID:11125103, RESID:AA0064] synonym: "(S)-2-methylamino-4-(methylsulfanyl)butanoic acid" EXACT PSI-MI-alternate [] synonym: "2-methylamino-4-(methylthio)butanoic acid" EXACT PSI-MI-alternate [] synonym: "[M:meth]" EXACT PSI-MI-alternate [] synonym: "methylmethionine" EXACT PSI-MI-short [] synonym: "MMT" EXACT PSI-MI-alternate [] synonym: "N-methyl-L-methionine" EXACT PSI-MI-alternate [] synonym: "N-methylmethionine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0169 name: n-methyl-phenylalanine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00074." [PMID:14755292] synonym: "(S)-2-methylamino-3-phenylpropanoic acid" EXACT PSI-MI-alternate [] synonym: "[F:meth]" EXACT PSI-MI-alternate [] synonym: "FMT" EXACT PSI-MI-alternate [] synonym: "methylphenylalanine" EXACT PSI-MI-short [] synonym: "N-methyl-L-phenylalanine" EXACT PSI-MI-alternate [] synonym: "N-methylphenylalanine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0170 name: phosphorylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00696." [PMID:11125103] synonym: "phosphorylated" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0171 name: omega-n-phospho-arginine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00227." [PMID:11125103, RESID:AA0222] synonym: "(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid" EXACT PSI-MI-alternate [] synonym: "[R:po]" EXACT PSI-MI-alternate [] synonym: "alpha-amino-delta-phosphonoguanidinovaleric acid" EXACT PSI-MI-alternate [] synonym: "N5-[imino(phosphonoamino)methyl]-L-ornithine" EXACT PSI-MI-alternate [] synonym: "omega-N-phospho-L-arginine" EXACT PSI-MI-alternate [] synonym: "phosphoarginine" EXACT PSI-MI-short [] synonym: "RPO" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0172 name: aspartic 4-phosphoric anhydride namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00042." [PMID:11125103, RESID:AA0033] synonym: "(S)-2-aminobutanedioic 4-phosphoric anhydride" EXACT PSI-MI-alternate [] synonym: "[D:po]" EXACT PSI-MI-alternate [] synonym: "beta-aspartyl phosphate" EXACT PSI-MI-alternate [] synonym: "DPO" EXACT PSI-MI-alternate [] synonym: "L-aspartic 4-phosphoric anhydride" EXACT PSI-MI-alternate [] synonym: "phosphoaspartic acid" EXACT PSI-MI-alternate [] synonym: "phosphoaspartic acid" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0173 name: s-phospho-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00043." [PMID:11125103, RESID:AA0034] synonym: "(R)-2-amino-3-(phosphonosulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "[C:po]" EXACT PSI-MI-alternate [] synonym: "CPO" EXACT PSI-MI-alternate [] synonym: "cysteine phosphate thioester" EXACT PSI-MI-alternate [] synonym: "phosphocysteine" EXACT PSI-MI-short [] synonym: "S-phospho-L-cysteine" EXACT PSI-MI-alternate [] synonym: "S-phosphonocysteine" EXACT PSI-MI-alternate [] synonym: "S3-phosphocysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0174 name: 1'-phospho-histidine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00044." [PMID:11125103, RESID:AA0035] synonym: "(S)-2-amino-3-(1-phosphono-1H-imidazol-4-yl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "1'-phospho-L-histidine" EXACT PSI-MI-alternate [] synonym: "1-phosphohistidine" EXACT PSI-MI-short [] synonym: "[H:po_e]" EXACT PSI-MI-alternate [] synonym: "histidine-3-phosphate [misnomer]" EXACT PSI-MI-alternate [] synonym: "histidine-N(epsilon)-phosphate" EXACT PSI-MI-alternate [] synonym: "histidine-N1'-phosphate" EXACT PSI-MI-alternate [] synonym: "HPE" EXACT PSI-MI-alternate [] synonym: "tau-phosphohistidine" EXACT PSI-MI-alternate [] synonym: "tele-phosphohistidine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0175 name: 3'-phospho-histidine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00045." [PMID:11125103, RESID:AA0036] synonym: "(S)-2-amino-3-(3-phosphono-3H-imidazol-4-yl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "3-phosphohistidine" EXACT PSI-MI-short [] synonym: "[H:po_d]" EXACT PSI-MI-alternate [] synonym: "histidine-1-phosphate [misnomer]" EXACT PSI-MI-alternate [] synonym: "histidine-N(delta)-phosphate" EXACT PSI-MI-alternate [] synonym: "histidine-N3'-phosphate" EXACT PSI-MI-alternate [] synonym: "HPD" EXACT PSI-MI-alternate [] synonym: "pi-phosphohistidine" EXACT PSI-MI-alternate [] synonym: "pros-phosphohistidine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0176 name: o-phospho-serine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00046." [PMID:11125103, RESID:AA0037] synonym: "(S)-2-amino-3-(phosphonooxy)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-hydroxypropanoic acid 3-phosphate" EXACT PSI-MI-alternate [] synonym: "2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine" EXACT PSI-MI-alternate [] synonym: "[S:po]" EXACT PSI-MI-alternate [] synonym: "O-phospho-L-serine" EXACT PSI-MI-alternate [] synonym: "O-phosphonoserine" EXACT PSI-MI-alternate [] synonym: "O3-phosphoserine" EXACT PSI-MI-alternate [] synonym: "phosphoserine" EXACT PSI-MI-short [] synonym: "serine phosphate ester" EXACT PSI-MI-alternate [] synonym: "SPO" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0177 name: o-phospho-threonine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00047." [PMID:11125103, RESID:AA0038] synonym: "(2S,3R)-2-amino-3-phosphonooxybutanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-hydroxybutanoic acid 3-phosphate" EXACT PSI-MI-alternate [] synonym: "[T:po]" EXACT PSI-MI-alternate [] synonym: "O-phospho-L-threonine" EXACT PSI-MI-alternate [] synonym: "O3-phosphothreonine" EXACT PSI-MI-alternate [] synonym: "phosphothreonine" EXACT PSI-MI-short [] synonym: "threonine phosphate ester" EXACT PSI-MI-alternate [] synonym: "TPO" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0178 name: o4'-phospho-tyrosine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00048." [PMID:11125103, RESID:AA0039] synonym: "(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate" EXACT PSI-MI-alternate [] synonym: "[Y:po]" EXACT PSI-MI-alternate [] synonym: "O4'-phospho-L-tyrosine" EXACT PSI-MI-alternate [] synonym: "O4-phosphotyrosine" EXACT PSI-MI-alternate [] synonym: "phosphotyrosine" EXACT PSI-MI-short [] synonym: "tyrosine phosphate" EXACT PSI-MI-alternate [] synonym: "YPO" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0179 name: other modification namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00032." [PMID:11125103] is_obsolete: true [Term] id: MI:0180 name: selenocysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00031." [PMID:11125103, RESID:AA0022] synonym: "3-selenylalanine" EXACT PSI-MI-alternate [] synonym: "[C:sel]" EXACT PSI-MI-alternate [] synonym: "CSE" EXACT PSI-MI-alternate [] synonym: "L-selenocysteine" EXACT PSI-MI-alternate [] synonym: "selenium cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0181 name: selenomethionine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00530." [PMID:11125103] synonym: "[M:sel]" EXACT PSI-MI-alternate [] synonym: "L-selenomethionine" EXACT PSI-MI-alternate [] synonym: "MSE" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0182 name: 3-oxoalanine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:01169." [PMID:11125103, RESID:AA0185] synonym: "(S)-2-amino-3-oxopropanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-oxopropionic acid" EXACT PSI-MI-alternate [] synonym: "[S:oxal]" EXACT PSI-MI-alternate [] synonym: "L-3-oxoalanine" EXACT PSI-MI-alternate [] synonym: "L-alpha-formylglycine" EXACT PSI-MI-alternate [] synonym: "L-amino-malonic acid semialdehyde" EXACT PSI-MI-alternate [] synonym: "L-aminomalonaldehydic acid" EXACT PSI-MI-alternate [] synonym: "L-serinesemialdehyde [misnomer]" EXACT PSI-MI-alternate [] synonym: "oxoalanine" EXACT PSI-MI-short [] synonym: "SOX" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0183 name: 2-pyrrolidone-5-carboxylic acid namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00040." [PMID:11125103, RESID:AA0031] synonym: "(S)-5-oxo-2-pyrrolidinecarboxylic acid" EXACT PSI-MI-alternate [] synonym: "2-oxopyrrolidine-5-carboxylic acid" EXACT PSI-MI-alternate [] synonym: "5-oxoproline" EXACT PSI-MI-alternate [] synonym: "5-oxopyrrolidine-2-carboxylic acid" EXACT PSI-MI-alternate [] synonym: "[E:pyro]" EXACT PSI-MI-alternate [] synonym: "pyroglutamic acid" EXACT PSI-MI-alternate [] synonym: "pyroglutamic acid" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0184 name: glutamyl 5-glycerylphosphorylethanolamine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00179." [PMID:11125103, RESID:AA0170] synonym: "(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid" EXACT PSI-MI-alternate [] synonym: "[E:gpe]" EXACT PSI-MI-alternate [] synonym: "EGE" EXACT PSI-MI-alternate [] synonym: "glycerylpo4etohamine" EXACT PSI-MI-short [] synonym: "L-glutamyl 5-glycerophosphoethanolamine" EXACT PSI-MI-alternate [] synonym: "L-glutamyl 5-glycerophosphorylethanolamine" EXACT PSI-MI-alternate [] synonym: "L-glutamyl 5-glycerylphosphorylethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0185 name: 2'-[3-carboxamido-3-(trimethylammonio)propyl]-histidine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00049." [PMID:11125103, RESID:AA0040] synonym: "2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine" EXACT PSI-MI-alternate [] synonym: "2-[(Xi)-3-carboxamido-3-(trimethylammonio)propyl]-4-((S)-2-amino-2-carboxyethyl)-1H-imidazole" EXACT PSI-MI-alternate [] synonym: "2-[3-carboxamido-3-(trimethylammonio)propyl]histidine" EXACT PSI-MI-alternate [] synonym: "2-amino-3-[[2-(3-amino-3-carbamoyl-prop-1-enyl)-1,1,3-trimethyl-2,3-dihydroimidazol-5-yl]]propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-4-[[5-(2-amino-2-carboxylato-ethyl)-1,1,3-trimethyl-2,3-dihydroimidazol-2-yl]]but-3-enamide" EXACT PSI-MI-alternate [] synonym: "[H:diph]" EXACT PSI-MI-alternate [] synonym: "alpha-(aminocarbonyl)-4-(2-amino-2-carboxyethyl)-N,N,N-trimethyl-1H-imidazole-2-propanaminium" EXACT PSI-MI-alternate [] synonym: "diphthamide" EXACT PSI-MI-alternate [] synonym: "diphthamide" EXACT PSI-MI-short [] synonym: "HDP" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0186 name: n6-biotinyl-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00126." [PMID:11125103, RESID:AA0117] synonym: "(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine" EXACT PSI-MI-alternate [] synonym: "(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:biotin]" EXACT PSI-MI-alternate [] synonym: "biocytin" EXACT PSI-MI-alternate [] synonym: "biotinyllysine" EXACT PSI-MI-short [] synonym: "epsilon-N-biotinyllysine" EXACT PSI-MI-alternate [] synonym: "KBT" EXACT PSI-MI-alternate [] synonym: "N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-biotinyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-biotinyllysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0187 name: n6-(4-amino-2-hydroxybutyl)-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00125." [PMID:11125103, RESID:AA0116] synonym: "(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:hypu]" EXACT PSI-MI-alternate [] synonym: "hypusine" EXACT PSI-MI-alternate [] synonym: "hypusine" EXACT PSI-MI-short [] synonym: "KHY" EXACT PSI-MI-alternate [] synonym: "N6-(4-amino-2-hydroxybutyl)-L-lysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0188 name: n6-retinal-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00129." [PMID:11125103, RESID:AA0120] synonym: "(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid" EXACT PSI-MI-alternate [] synonym: "[K:retin]" EXACT PSI-MI-alternate [] synonym: "KRT" EXACT PSI-MI-alternate [] synonym: "N6-retinal-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-retinyl-lysine" EXACT PSI-MI-alternate [] synonym: "N6-retinylidene-L-lysine" EXACT PSI-MI-alternate [] synonym: "retinallysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0189 name: ubiquitinated lysine namespace: PSI-MI def: "Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein.\nOBSOLETE remap to MOD:00134." [PMID:11125103, RESID:AA0125] synonym: "[K:ub]" EXACT PSI-MI-alternate [] synonym: "KUB" EXACT PSI-MI-alternate [] synonym: "N6-glycyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-glycyllysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0190 name: interaction type namespace: PSI-MI def: "Connection between molecule." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0191 name: aggregation namespace: PSI-MI def: "Physical association among molecules.\nOBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0192 name: acetylation reaction namespace: PSI-MI def: "Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues." [GO:0006473, PMID:14755292, RESID:AA0041, RESID:AA0042, RESID:AA0043, RESID:AA0044, RESID:AA0045, RESID:AA0046, RESID:AA0047, RESID:AA0048, RESID:AA0049, RESID:AA0050, RESID:AA0051, RESID:AA0052, RESID:AA0053, RESID:AA0054, RESID:AA0055, RESID:AA0056] subset: PSI-MI_slim synonym: "acetylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0193 name: amidation reaction namespace: PSI-MI def: "Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues." [GO:0001519, PMID:14755292, RESID:AA0081, RESID:AA0082, RESID:AA0083, RESID:AA0084, RESID:AA0085, RESID:AA0086, RESID:AA0087, RESID:AA0088, RESID:AA0089, RESID:AA0090, RESID:AA0091, RESID:AA0092, RESID:AA0093, RESID:AA0094, RESID:AA0095, RESID:AA0096, RESID:AA0097, RESID:AA0098, RESID:AA0099, RESID:AA0100] subset: PSI-MI_slim synonym: "amidation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0194 name: cleavage reaction namespace: PSI-MI def: "Covalent bond breakage in a molecule leading to the formation of smaller molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "cleavage" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0195 name: covalent binding namespace: PSI-MI def: "Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0407 ! direct interaction [Term] id: MI:0196 name: covalent interaction namespace: PSI-MI def: "Physical interaction mediated by covalent bond rearrangement.\nOBSOLETE use covalent binding (MI:0195) instead." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0197 name: deacetylation reaction namespace: PSI-MI def: "N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues." [GO:0006476, PMID:14755292, RESID:AA0055, RESID:AA0056] subset: PSI-MI_slim synonym: "deacetylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0198 name: defarnesylation reaction namespace: PSI-MI def: "S-farnesyl-L-cysteined is cleaved and returns a C residue." [PMID:14755292, RESID:AA0102] subset: PSI-MI_slim synonym: "defarnesylation" EXACT PSI-MI-short [] is_a: MI:0212 ! lipid cleavage reaction [Term] id: MI:0199 name: deformylation reaction namespace: PSI-MI def: "N6-formyl-L-lysine is cleaved and returns a K residue." [PMID:14755292, RESID:AA0211] subset: PSI-MI_slim synonym: "deformylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0200 name: degeranylation reaction namespace: PSI-MI def: "S-geranylgeranyl-L-cysteine is cleaved and returns a C residue." [PMID:14755292, RESID:AA0104] subset: PSI-MI_slim synonym: "degeranylation" EXACT PSI-MI-short [] is_a: MI:0212 ! lipid cleavage reaction [Term] id: MI:0201 name: demyristoylation reaction namespace: PSI-MI def: "N6-myristoyl-L-lysine is cleaved and returns a K residue." [PMID:14755292, RESID:AA0078] subset: PSI-MI_slim synonym: "demyristoylation" EXACT PSI-MI-short [] is_a: MI:0212 ! lipid cleavage reaction [Term] id: MI:0202 name: depalmitoylation reaction namespace: PSI-MI def: "S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues." [PMID:14755292, RESID:AA0060, RESID:AA0077, RESID:AA0106] subset: PSI-MI_slim synonym: "depalmitoylation" EXACT PSI-MI-short [] is_a: MI:0212 ! lipid cleavage reaction [Term] id: MI:0203 name: dephosphorylation reaction namespace: PSI-MI def: "Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues." [GO:0016311, PMID:14755292, RESID:AA0033, RESID:AA0034, RESID:AA0035, RESID:AA0036, RESID:AA0037, RESID:AA0038, RESID:AA0039, RESID:AA0222] subset: PSI-MI_slim synonym: "dephosphorylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0204 name: deubiquitination reaction namespace: PSI-MI def: "Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins." [GO:0016579, PMID:11583613, RESID:AA0125] subset: PSI-MI_slim synonym: "deubiquitination" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0205 name: disaggregation namespace: PSI-MI def: "Dissociation of partners interacting via non-covalent bond.\nOBSOLETE because considered misleading." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0206 name: farnesylation reaction namespace: PSI-MI def: "Reversible reaction that can affect C residue." [GO:0018347, PMID:14755292, RESID:AA0102] subset: PSI-MI_slim synonym: "farnesylation" EXACT PSI-MI-short [] is_a: MI:0211 ! lipid addition [Term] id: MI:0207 name: formylation reaction namespace: PSI-MI def: "Reaction that can affect K or G residues. Reside is functionalised with a formyl group." [GO:0018256, PMID:14755292, RESID:AA0057, RESID:AA0211] subset: PSI-MI_slim synonym: "formylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0208 name: genetic interaction namespace: PSI-MI def: "Two genes A and B \"genetically interact\" when the phenotype generated as the result of mutations in both genes (double mutant ab) is unexpectedly not just a combination of the phenotypes of the two single mutants a and b." [PMID:16527956] subset: PSI-MI_slim is_a: MI:0190 ! interaction type [Term] id: MI:0209 name: geranylgeranylation reaction namespace: PSI-MI def: "Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue." [GO:0018348, PMID:14755292, RESID:AA0104] subset: PSI-MI_slim synonym: "geranylgeranylation" EXACT PSI-MI-short [] is_a: MI:0211 ! lipid addition [Term] id: MI:0210 name: hydroxylation reaction namespace: PSI-MI def: "Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds." [GO:0018126, PMID:14755292, RESID:AA0028, RESID:AA0029, RESID:AA0030, RESID:AA0146, RESID:AA0215] subset: PSI-MI_slim synonym: "hydroxylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0211 name: lipid addition namespace: PSI-MI def: "Covalent or non covalent binding of lipid group on a protein residue." [GO:0006497, PMID:14755292] subset: PSI-MI_slim is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0212 name: lipid cleavage reaction namespace: PSI-MI def: "Cleavage of a lipid group covalently bound to a protein residue." [PMID:14755292] subset: PSI-MI_slim synonym: "lipid cleavage" EXACT PSI-MI-short [] is_a: MI:0194 ! cleavage reaction [Term] id: MI:0213 name: methylation reaction namespace: PSI-MI def: "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues." [GO:0043414, PMID:14755292, RESID:AA0061, RESID:AA0062, RESID:AA0063, RESID:AA0064, RESID:AA0065, RESID:AA0066, RESID:AA0067, RESID:AA0068, RESID:AA0069, RESID:AA0070, RESID:AA0071, RESID:AA0072, RESID:AA0073, RESID:AA0074, RESID:AA0075, RESID:AA0076, RESID:AA0234, RESID:AA0272] subset: PSI-MI_slim synonym: "methylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0214 name: myristoylation reaction namespace: PSI-MI def: "Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues." [GO:0018319, PMID:14755292, RESID:AA0059, RESID:AA0078] subset: PSI-MI_slim synonym: "myristoylation" EXACT PSI-MI-short [] is_a: MI:0211 ! lipid addition [Term] id: MI:0215 name: non covalent interaction namespace: PSI-MI def: "Interaction mediated by non-covalent, weak forces rearrangement.\nOBSOLETE use physical interaction (MI:0218) instead." [PMID:14755292] subset: PSI-MI_slim synonym: "non covalent inter" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0216 name: palmitoylation reaction namespace: PSI-MI def: "Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues." [GO:0018318, PMID:14755292, RESID:AA0060, RESID:AA0077, RESID:AA0079, RESID:AA0080, RESID:AA0106] subset: PSI-MI_slim synonym: "palmitoylation" EXACT PSI-MI-short [] is_a: MI:0211 ! lipid addition [Term] id: MI:0217 name: phosphorylation reaction namespace: PSI-MI def: "Reversible reaction that can affect D,C,H,S,T,Y,R residues." [GO:0016310, PMID:14755292, RESID:AA0033, RESID:AA0034, RESID:AA0035, RESID:AA0036, RESID:AA0037, RESID:AA0038, RESID:AA0039, RESID:AA0222] subset: PSI-MI_slim synonym: "phosphorylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0218 name: physical interaction namespace: PSI-MI def: "Interaction among molecules that can be direct or indirect.\nOBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915." [PMID:14755292] is_obsolete: true [Term] id: MI:0219 name: synthetic lethal namespace: PSI-MI def: "Death phenotype observed on cells carrying combination of two independently silent mutations.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)" [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0220 name: ubiquitination reaction namespace: PSI-MI def: "Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target." [GO:0016567, PMID:11583613, RESID:AA0125] subset: PSI-MI_slim synonym: "ubiquitination" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0221 name: expression level namespace: PSI-MI def: "Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0346 ! experimental preparation [Term] id: MI:0222 name: physiological level namespace: PSI-MI def: "A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate." [PMID:14755292] subset: PSI-MI_slim synonym: "endogenous" EXACT PSI-MI-alternate [] synonym: "endogenous level" EXACT PSI-MI-alternate [] is_a: MI:0221 ! expression level [Term] id: MI:0223 name: under expressed level namespace: PSI-MI def: "A molecule is estimated to be expressed at lower levels than in physiological condition." [PMID:14755292] subset: PSI-MI_slim synonym: "under-expressed" EXACT PSI-MI-short [] is_a: MI:0221 ! expression level is_a: MI:0803 ! expression level alteration [Term] id: MI:0225 name: chromatin immunoprecipitation array namespace: PSI-MI def: "The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus." [PMID:11125145, PMID:11206552] subset: PSI-MI_slim synonym: "chip-chip" EXACT PSI-MI-short [] is_a: MI:0008 ! array technology is_a: MI:0402 ! chromatin immunoprecipitation assay [Term] id: MI:0226 name: ion exchange chromatography namespace: PSI-MI def: "Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns." [PMID:14755292] subset: PSI-MI_slim synonym: "IEC" EXACT PSI-MI-alternate [] synonym: "ion exchange chrom" EXACT PSI-MI-short [] is_a: MI:0091 ! chromatography technology [Term] id: MI:0227 name: reverse phase chromatography namespace: PSI-MI def: "Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds." [PMID:14755292] subset: PSI-MI_slim synonym: "reverse phase chrom" EXACT PSI-MI-short [] is_a: MI:0091 ! chromatography technology [Term] id: MI:0228 name: cytoplasmic complementation assay namespace: PSI-MI def: "Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay" [PMID:14755292] subset: PSI-MI_slim synonym: "cytoplasmic compl" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0230 name: membrane bound complementation assay namespace: PSI-MI def: "OBSOLETE remap to MI:0090 protein complementation assay." [PMID:14755292] subset: PSI-MI_slim synonym: "membrane compl" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0231 name: mammalian protein protein interaction trap namespace: PSI-MI def: "The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions." [PMID:12853652] subset: PSI-MI_slim synonym: "mappit" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0232 name: transcriptional complementation assay namespace: PSI-MI def: "Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression." [PMID:14755292] subset: PSI-MI_slim synonym: "transcription compl" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0233 name: protein dna complex namespace: PSI-MI def: "A stable set of interacting protein and DNA that can be copurified and operate as a functional unit." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0314 ! complex [Term] id: MI:0234 name: 131i radiolabel namespace: PSI-MI def: "Molecule labelled with 131 radio isotope of iodine atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "131I" EXACT PSI-MI-alternate [] synonym: "I131" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0235 name: 14c radiolabel namespace: PSI-MI def: "Molecule labelled with the radio isotope 14 of carbon atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "14C" EXACT PSI-MI-alternate [] synonym: "C14" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0236 name: 32p radiolabel namespace: PSI-MI def: "Molecule labelled with the radio isotope 32 of phosphorus atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "32P" EXACT PSI-MI-alternate [] synonym: "P32" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0237 name: 33p radiolabel namespace: PSI-MI def: "Molecule labelled with the radio isotope 33 of phosphorus atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "33P" EXACT PSI-MI-alternate [] synonym: "P33" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0238 name: 3h radiolabel namespace: PSI-MI def: "Molecules labelled with isotope 3 of hydrogen atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "3H" EXACT PSI-MI-alternate [] synonym: "H3" EXACT PSI-MI-alternate [] synonym: "tritium" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0239 name: biotin tag namespace: PSI-MI def: "Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag [Term] id: MI:0240 name: fusion protein namespace: PSI-MI def: "The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag [Term] id: MI:0241 name: horseradish peroxidase tag namespace: PSI-MI def: "Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein." [PMID:14755292] subset: PSI-MI_slim synonym: "hrp tag" EXACT PSI-MI-short [] is_a: MI:0365 ! enzyme tag [Term] id: MI:0242 name: gene ontology definition reference namespace: PSI-MI def: "This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference." [PMID:14755292] subset: PSI-MI_slim synonym: "go-definition-ref" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0243 name: isoform parent sequence reference namespace: PSI-MI def: "Reference to the master sequence from which this isoform has been derived." [PMID:14755292] subset: PSI-MI_slim synonym: "isoform-parent" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0244 name: reactome complex namespace: PSI-MI def: "Collection of functional complexes within Reactome - a knowledgebase of biological processes.\nhttp://www.reactome.org/" [PMID:21067998] subset: PSI-MI_slim xref: id-validation-regexp:\"REACT_[0-9\]\{1\,5}\\.[0-9\]\{1\,3}|[0-9\]+\" xref: search-url: "http://www.reactome.org/cgi-bin/eventbrowser?ID=${ac}" is_a: MI:0467 ! reactome [Term] id: MI:0245 name: reactome protein namespace: PSI-MI def: "Collection of protein within the Reactome database - a knowledgebase of biological processes.\nhttp://www.reactome.org/" [PMID:21067998] subset: PSI-MI_slim xref: id-validation-regexp:\"REACT_[0-9\]\{1\,4}\\.[0-9\]\{1\,3}|[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]|[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]-[0-9\]+|[A-Z\]\{3}[0-9\]\{5}|[OPQ\][0-9\][A-Z0-9\]\{3}[0-9\]-PRO_[0-9\]\{10}\" xref: search-url: "http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=${ac}" is_a: MI:0467 ! reactome [Term] id: MI:0246 name: cabri namespace: PSI-MI def: "CABRI cell lines catalogue available at.\nhttp://www.cabri.org/" [PMID:14755292] subset: PSI-MI_slim xref: id-validation-regexp:\"[0-9\]+|ACC\\s[A-Z0-9\]+|ECACC\\s[A-Z0-9\]+|LMBP\\s[A-Z0-9\]+|ICLC\\s[A-Z0-9\]+|CIP-[0-9\]+|DSMZ_MUTZ\\\:ACC\\s[0-9\]+ \" xref: search-url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[libs%3d{dsmz_mutz%20ecacc_cell%20iclc%20CABI_BACT%20CIP_BACT%20CABI_YEAST%20DSMZ_PLANT_CELL}-id:${ac}]+-e" is_a: MI:0473 ! participant database [Term] id: MI:0247 name: newt namespace: PSI-MI def: "New EBI Web Taxonomy.\nhttp://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942" [PMID:14755292] subset: PSI-MI_slim xref: id-validation-regexp:\"[0-9\]+\" xref: search-url: "http://www.ebi.ac.uk/newt/display?search=${ac}" is_obsolete: true [Term] id: MI:0248 name: resid namespace: PSI-MI def: "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.\nhttp://www.ebi.ac.uk/RESID/index.html" [PMID:14755292] subset: PSI-MI_slim xref: id-validation-regexp:\"AA[0-9\]\{4}\" xref: search-url: "http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e" is_a: MI:0447 ! feature database [Term] id: MI:0249 name: huge namespace: PSI-MI def: "A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project.\nhttp://www.kazusa.or.jp/huge/" [PMID:14755292] subset: PSI-MI_slim xref: id-validation-regexp:\"KIAA[0-9\]\{4}[A-Z\]\{0\,1}\" xref: search-url: "http://www.kazusa.or.jp/huge/gfpage/${ac}" is_a: MI:0683 ! sequence database [Term] id: MI:0250 name: gene namespace: PSI-MI def: "interactor for genetic interaction." [PMID:14755292, SO:0000704] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0251 name: gene product namespace: PSI-MI def: "Reference of a protein object pointing to its genomic or nucleic acid sequence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0252 name: biological feature namespace: PSI-MI def: "Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0116 ! feature type [Term] id: MI:0253 name: isotope label namespace: PSI-MI def: "One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0254 name: genetic interference namespace: PSI-MI def: "This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0255 name: post transcriptional interference namespace: PSI-MI def: "This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself." [PMID:14755292] subset: PSI-MI_slim synonym: "expression interfer" EXACT PSI-MI-short [] is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0256 name: rna interference namespace: PSI-MI def: "RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA." [PMID:12110901, PMID:12408823] subset: PSI-MI_slim synonym: "rnai" EXACT PSI-MI-short [] is_a: MI:0255 ! post transcriptional interference [Term] id: MI:0257 name: antisense rna namespace: PSI-MI def: "This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation." [PMID:1340158] subset: PSI-MI_slim is_a: MI:0255 ! post transcriptional interference [Term] id: MI:0258 name: inhibitor antibodies namespace: PSI-MI def: "Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm.\nOBSOLETE as such method can be described using the biological role inhibitor (MI:0586)." [PMID:10189716] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0259 name: perturbagens peptides namespace: PSI-MI def: "This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein.\nOBSOLETE as such method can be described using the biological role inhibitor (MI:0586)." [PMID:11731788, PMID:8606778] subset: PSI-MI_slim synonym: "perturbagens pep" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0260 name: inhibitor small molecules namespace: PSI-MI def: "Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'.\nOBSOLETE as such method can be described using the biological role inhibitor (MI:0586)." [PMID:10542155, PMID:10780927] subset: PSI-MI_slim synonym: "inhibitor small mol" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0261 name: suppression namespace: PSI-MI def: "A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793." [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0262 name: suppression mutation namespace: PSI-MI def: "A given (suppressed) mutation phenotype is reverted by a supressor gene mutation.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804. " [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0263 name: suppression knockout namespace: PSI-MI def: "Knocked out gene is the suppressor of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppress knockout" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0264 name: suppression partial alteration namespace: PSI-MI def: "A mutation is the partial suppressor of a mutant phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppression partial" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0265 name: suppression expression alteration namespace: PSI-MI def: "An altered expression is the suppressor of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppress expression" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0266 name: suppression overexpression namespace: PSI-MI def: "Overexpression is the suppressor of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppress overexpress" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0267 name: suppression scalable namespace: PSI-MI def: "Level of over/underexpression scales the 'extend' of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803. " [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0268 name: suppression underexpression namespace: PSI-MI def: "Underexpression is the suppressor of a phenotype.\nOBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223. " [PMID:15608217] subset: PSI-MI_slim synonym: "suppress underexpres" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0269 name: synthetic phenotype namespace: PSI-MI def: "Two silent mutations show an altered phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794." [PMID:15608217] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0270 name: conditional synthetic lethal namespace: PSI-MI def: "Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)" [PMID:15608217] subset: PSI-MI_slim synonym: "cond syntetic lethal" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0271 name: conditional synthetic lethal temperature-sensitivity namespace: PSI-MI def: "Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')" [PMID:15608217] subset: PSI-MI_slim synonym: "temprtr synt lethal" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0273 name: synthetic growth effect namespace: PSI-MI def: "Two silent mutations show altered growth effect when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')" [PMID:15608217] subset: PSI-MI_slim synonym: "synt growth effect" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0274 name: synthetic growth defect namespace: PSI-MI def: "Two silent mutations show growth defect when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')" [PMID:15608217] subset: PSI-MI_slim synonym: "synt growth defect" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0275 name: synthetic growth increase namespace: PSI-MI def: "Two silent mutations show growth increase when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')" [PMID:15608217] subset: PSI-MI_slim synonym: "synt growth increase" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0276 name: blue native page namespace: PSI-MI def: "Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE." [PMID:14665681] subset: PSI-MI_slim synonym: "bn-page" EXACT PSI-MI-short [] is_a: MI:0404 ! comigration in non denaturing gel electrophoresis [Term] id: MI:0300 name: alias type namespace: PSI-MI def: "Descriptor of type of nomenclature used to describe interactor." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "CvAliasType" EXACT PSI-MI-alternate [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0301 name: gene name namespace: PSI-MI def: "Gene name." [PMID:14755292] subset: PSI-MI_slim synonym: "gene" EXACT PSI-MI-alternate [] is_a: MI:1041 ! synonym [Term] id: MI:0302 name: gene name synonym namespace: PSI-MI def: "Gene name synonym." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1041 ! synonym [Term] id: MI:0303 name: gene ontology synonym namespace: PSI-MI def: "Synonym as used in Gene Ontology." [PMID:14755292] subset: PSI-MI_slim synonym: "go synonym" EXACT PSI-MI-short [] is_a: MI:1041 ! synonym [Term] id: MI:0304 name: isoform synonym namespace: PSI-MI def: "Isoform synonym." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1041 ! synonym [Term] id: MI:0305 name: ordered locus name namespace: PSI-MI def: "A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features." [PMID:14755292] comment: For instance HI0934, Rv3245c, At5g34500, YER456W. subset: PSI-MI_slim synonym: "CDS number" EXACT PSI-MI-alternate [] synonym: "locus name" EXACT PSI-MI-short [] synonym: "ONL" EXACT PSI-MI-alternate [] synonym: "Ordered locus name" EXACT PSI-MI-alternate [] synonym: "ORF number" EXACT PSI-MI-alternate [] synonym: "systematic gene number" EXACT PSI-MI-alternate [] is_a: MI:1041 ! synonym [Term] id: MI:0306 name: open reading frame name namespace: PSI-MI def: "A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system." [PMID:14755292] comment: For instance MtCY277-28c, SYGP-ORF50, SpBC2F12-04, C06E1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames. subset: PSI-MI_slim synonym: "orf name" EXACT PSI-MI-short [] is_a: MI:1041 ! synonym [Term] id: MI:0307 name: delivery method namespace: PSI-MI def: "Method by which molecule is delivered or engineered into a cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0346 ! experimental preparation [Term] id: MI:0308 name: electroporation namespace: PSI-MI def: "Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm." [PMID:6329708] subset: PSI-MI_slim is_a: MI:0307 ! delivery method [Term] id: MI:0309 name: genomic tagging namespace: PSI-MI def: "A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control.\nOBSOLETE redundant term. Map to feature type : tag (MI:0507)." [PMID:14755292] subset: PSI-MI_slim synonym: "genetic tag insertion" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0310 name: infection namespace: PSI-MI def: "Molecule introduced into a cell via an external organism, usually a virus or bacteria." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0307 ! delivery method [Term] id: MI:0311 name: microinjection namespace: PSI-MI def: "The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed." [PMID:3016916] subset: PSI-MI_slim synonym: "micro-injection" EXACT PSI-MI-alternate [] is_a: MI:0307 ! delivery method [Term] id: MI:0312 name: nucleic acid transfection namespace: PSI-MI def: "Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient \"holes\" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl transfection" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0313 name: interactor type namespace: PSI-MI def: "Molecular species involved in the interaction." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "participant type" EXACT PSI-MI-alternate [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0314 name: complex namespace: PSI-MI def: "Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0315 name: protein complex namespace: PSI-MI def: "A stable set of interacting proteins that can be copurified and operate as a functional unit." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0314 ! complex [Term] id: MI:0316 name: ribonucleoprotein complex namespace: PSI-MI def: "A macromolecular complex containing both protein and RNA molecules." [GO:0030529, PMID:14755292] subset: PSI-MI_slim synonym: "protein rna complex" EXACT PSI-MI-alternate [] synonym: "ribonucleoprot compl" EXACT PSI-MI-short [] is_a: MI:0314 ! complex [Term] id: MI:0317 name: interaction namespace: PSI-MI def: "Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0318 name: nucleic acid namespace: PSI-MI def: "Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages." [PMID:14755292, SO:0000348] subset: PSI-MI_slim is_a: MI:0383 ! biopolymer [Term] id: MI:0319 name: deoxyribonucleic acid namespace: PSI-MI def: "Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine." [PMID:14755292, SO:0000352] subset: PSI-MI_slim synonym: "deoxyribonucleic acid" EXACT PSI-MI-alternate [] synonym: "DNA" EXACT PSI-MI-alternate [] synonym: "dna" EXACT PSI-MI-short [] is_a: MI:0318 ! nucleic acid [Term] id: MI:0320 name: ribonucleic acid namespace: PSI-MI def: "Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine." [PMID:14755292, SO:0000356] subset: PSI-MI_slim synonym: "RNA" EXACT PSI-MI-alternate [] synonym: "rna" EXACT PSI-MI-short [] is_a: MI:0318 ! nucleic acid [Term] id: MI:0321 name: catalytic rna namespace: PSI-MI def: "Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link." [PMID:14755292] subset: PSI-MI_slim synonym: "catalytic ribonucleic acid" EXACT PSI-MI-alternate [] synonym: "catalytic RNA" EXACT PSI-MI-alternate [] synonym: "crna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0322 name: guide rna namespace: PSI-MI def: "Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing." [PMID:14755292] subset: PSI-MI_slim synonym: "grna" EXACT PSI-MI-short [] synonym: "guide RNA" EXACT PSI-MI-alternate [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0323 name: heterogeneous nuclear rna namespace: PSI-MI def: "A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein." [PMID:14755292] subset: PSI-MI_slim synonym: "heterogeneous nuclear ribonucleic acid" EXACT PSI-MI-alternate [] synonym: "heterogeneous nuclear RNA" EXACT PSI-MI-alternate [] synonym: "hnrna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0324 name: messenger rna namespace: PSI-MI def: "Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains." [PMID:14755292] subset: PSI-MI_slim synonym: "mRNA" EXACT PSI-MI-alternate [] synonym: "mrna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0325 name: transfer rna namespace: PSI-MI def: "The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon." [PMID:14755292] subset: PSI-MI_slim synonym: "transfer ribonucleic acid" EXACT PSI-MI-alternate [] synonym: "transfer RNA" EXACT PSI-MI-alternate [] synonym: "tRNA" EXACT PSI-MI-alternate [] synonym: "trna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0326 name: protein namespace: PSI-MI def: "A linear polymer of amino acids joined by peptide bonds in a specific sequence." [PMID:14755292, SO:0000358] subset: PSI-MI_slim is_a: MI:0383 ! biopolymer [Term] id: MI:0327 name: peptide namespace: PSI-MI def: "Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues." [PMID:14755292] subset: PSI-MI_slim synonym: "oligopeptide" EXACT PSI-MI-alternate [] synonym: "polypeptide" EXACT PSI-MI-alternate [] is_a: MI:0383 ! biopolymer [Term] id: MI:0328 name: small molecule namespace: PSI-MI def: "Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [PMID:14755292] subset: Drugable subset: PSI-MI_slim is_a: MI:1100 ! bioactive entity [Term] id: MI:0329 name: unknown participant namespace: PSI-MI def: "Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0330 name: molecular source namespace: PSI-MI def: "Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process." [PMID:14755272] subset: PSI-MI_slim is_a: MI:0346 ! experimental preparation [Term] id: MI:0331 name: engineered namespace: PSI-MI def: "Molecule has been added into system from an external source or altered within the cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0330 ! molecular source [Term] id: MI:0332 name: naturally occurring namespace: PSI-MI def: "Unaltered endogenous molecule in its naturally occurring state." [PMID:14755292] subset: PSI-MI_slim synonym: "endogenous" EXACT PSI-MI-alternate [] is_a: MI:0330 ! molecular source [Term] id: MI:0333 name: feature range status namespace: PSI-MI def: "Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range." [PMID:14755292] subset: PSI-MI_slim synonym: "CvFuzzyType" EXACT PSI-MI-alternate [] synonym: "endStatus" EXACT PSI-MI-alternate [] synonym: "startStatus" EXACT PSI-MI-alternate [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0334 name: c-terminal position namespace: PSI-MI def: "Term describing the last amino acid of a peptide chain." [PMID:14755292] comment: Displayed as 'c'. subset: PSI-MI_slim synonym: "c-term" EXACT PSI-MI-alternate [] synonym: "c-terminal" EXACT PSI-MI-short [] synonym: "c-terminus" EXACT PSI-MI-alternate [] synonym: "carboxy-terminus" EXACT PSI-MI-alternate [] is_a: MI:0333 ! feature range status [Term] id: MI:0335 name: certain sequence position namespace: PSI-MI def: "Position within the sequence clearly defined." [PMID:14755292] subset: PSI-MI_slim synonym: "certain" EXACT PSI-MI-short [] is_a: MI:0333 ! feature range status [Term] id: MI:0336 name: greater-than namespace: PSI-MI def: "Partially determined sequence position known to be in a location higher than a given position." [PMID:14755292] comment: Displayed as '>'. subset: PSI-MI_slim is_a: MI:0333 ! feature range status [Term] id: MI:0337 name: less-than namespace: PSI-MI def: "Partially determined sequence position known to be in a position lower than a given position." [PMID:14755292] comment: Displayed as '<'. subset: PSI-MI_slim is_a: MI:0333 ! feature range status [Term] id: MI:0338 name: range namespace: PSI-MI def: "Describes a sequence position known to be in a certain range, where the exact position is unclear." [PMID:14755292] comment: For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'. subset: PSI-MI_slim is_a: MI:0333 ! feature range status [Term] id: MI:0339 name: undetermined sequence position namespace: PSI-MI def: "Term describing a completely unknown or unspecified sequence position." [PMID:14755292] comment: Displayed as '?'. subset: PSI-MI_slim synonym: "undetermined" EXACT PSI-MI-short [] is_a: MI:0333 ! feature range status [Term] id: MI:0340 name: n-terminal position namespace: PSI-MI def: "Term describing the first amino acid of a peptide chain." [PMID:14755292] comment: Displayed as 'n'. subset: PSI-MI_slim synonym: "amino-terminus" EXACT PSI-MI-alternate [] synonym: "n-term" EXACT PSI-MI-alternate [] synonym: "n-terminal " EXACT PSI-MI-short [] synonym: "n-terminus" EXACT PSI-MI-alternate [] is_a: MI:0333 ! feature range status [Term] id: MI:0341 name: ragged n-terminus namespace: PSI-MI def: "Mixture of protein forms where N-terminus has been progressively truncated." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0340 ! n-terminal position [Term] id: MI:0342 name: sample process namespace: PSI-MI def: "Indicates the sample context in which each interacting molecule is presented to its partner." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0346 ! experimental preparation [Term] id: MI:0343 name: cdna library namespace: PSI-MI def: "Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process." [PMID:6110205] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0344 name: cell lysate namespace: PSI-MI def: "Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0345 name: author assigned name namespace: PSI-MI def: "Name assigned to a molecule by the authors within a paper that may differ from the reference database." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1041 ! synonym [Term] id: MI:0346 name: experimental preparation namespace: PSI-MI def: "Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental prep" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0348 name: fixed cell namespace: PSI-MI def: "Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0349 name: living cell namespace: PSI-MI def: "Molecule is observed within in a living cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0350 name: purified namespace: PSI-MI def: "Molecule has undergone one or more purification steps to isolate it from the cellular environment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0342 ! sample process [Term] id: MI:0351 name: homogeneous namespace: PSI-MI def: "The author states a molecule is completely pure, i.e. no other molecular species are present." [PMID:14755292] subset: PSI-MI_slim synonym: "pure" EXACT PSI-MI-alternate [] is_a: MI:0350 ! purified [Term] id: MI:0352 name: partially purified namespace: PSI-MI def: "The author states a molecule is only partially purified, i.e. other molecular species also known to be present." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0350 ! purified [Term] id: MI:0353 name: cross-reference type namespace: PSI-MI def: "Qualifier to describe the type of information a cross-reference is pointing to." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "CvXrefQualifier" EXACT PSI-MI-alternate [] synonym: "refType" EXACT PSI-MI-alternate [] synonym: "xref type" EXACT PSI-MI-short [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0354 name: gene ontology term for cellular component namespace: PSI-MI def: "Cross reference pointing to a Gene Ontology -'cellular component' term." [PMID:14681407] subset: PSI-MI_slim synonym: "component" EXACT PSI-MI-short [] synonym: "go component term" EXACT PSI-MI-alternate [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0355 name: gene ontology term for cellular function namespace: PSI-MI def: "Cross reference pointing to a Gene Ontology -'cellular function' term." [PMID:14681407] subset: PSI-MI_slim synonym: "function" EXACT PSI-MI-short [] synonym: "go function term" EXACT PSI-MI-alternate [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0356 name: identical object namespace: PSI-MI def: "Reference to the corresponding object in another database. Correspondence may be complete or partial." [PMID:14755292] comment: For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database. subset: Drugable subset: PSI-MI_slim synonym: "identity" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0357 name: method reference namespace: PSI-MI def: "Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0358 name: primary-reference namespace: PSI-MI def: "Used to indicate the PMID from which the experimental data is extracted." [PMID:14755292] subset: Drugable subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0359 name: gene ontology term for cellular process namespace: PSI-MI def: "Cross reference pointing to a Gene Ontology -'cellular process' term." [PMID:14681407] subset: PSI-MI_slim synonym: "go process term" EXACT PSI-MI-alternate [] synonym: "process" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0360 name: secondary accession number namespace: PSI-MI def: "Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number." [PMID:14755292] subset: PSI-MI_slim synonym: "secondary-ac" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0361 name: see-also namespace: PSI-MI def: "Related object within the same database or pointing to an external database." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0362 name: inference namespace: PSI-MI def: "Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "modeled" EXACT PSI-MI-alternate [] synonym: "modelled" EXACT PSI-MI-alternate [] is_a: MI:0001 ! interaction detection method is_a: MI:0002 ! participant identification method is_a: MI:0003 ! feature detection method [Term] id: MI:0363 name: inferred by author namespace: PSI-MI def: "Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "modeled by author" EXACT PSI-MI-alternate [] synonym: "modelled by author" EXACT PSI-MI-alternate [] is_a: MI:0362 ! inference [Term] id: MI:0364 name: inferred by curator namespace: PSI-MI def: "Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "modeled by curator" EXACT PSI-MI-alternate [] synonym: "modelled by curator" EXACT PSI-MI-alternate [] is_a: MI:0362 ! inference [Term] id: MI:0365 name: enzyme tag namespace: PSI-MI def: "Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein." [PMID:10935637] subset: PSI-MI_slim is_a: MI:0240 ! fusion protein [Term] id: MI:0366 name: alkaline phosphatase tag namespace: PSI-MI def: "Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein." [PMID:10935637] subset: PSI-MI_slim synonym: "alk phosphatase tag" EXACT PSI-MI-short [] is_a: MI:0365 ! enzyme tag [Term] id: MI:0367 name: green fluorescent protein tag namespace: PSI-MI def: "The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:7491768] subset: PSI-MI_slim synonym: "GFP" EXACT PSI-MI-alternate [] synonym: "gfp tag" EXACT PSI-MI-short [] synonym: "green fluorescent protein" EXACT PSI-MI-alternate [] is_a: MI:0687 ! fluorescent protein tag [Term] id: MI:0368 name: yellow fluorescent protein tag namespace: PSI-MI def: "Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:10929120] subset: PSI-MI_slim synonym: "yellow fluorescent protein" EXACT PSI-MI-alternate [] synonym: "YFP" EXACT PSI-MI-alternate [] synonym: "yfp tag" EXACT PSI-MI-short [] is_a: MI:0687 ! fluorescent protein tag [Term] id: MI:0369 name: lex-a dimerization assay namespace: PSI-MI def: "The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system." [PMID:12446730] subset: PSI-MI_slim synonym: "gallex" EXACT PSI-MI-alternate [] synonym: "gallex" EXACT PSI-MI-short [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0370 name: tox-r dimerization assay namespace: PSI-MI def: "This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts." [PMID:9927659] subset: PSI-MI_slim synonym: "toxcat" EXACT PSI-MI-alternate [] synonym: "toxcat" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0371 name: 35s radiolabel namespace: PSI-MI def: "Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium." [PMID:14755292] subset: PSI-MI_slim synonym: "35S" EXACT PSI-MI-alternate [] synonym: "S35" EXACT PSI-MI-alternate [] synonym: "s35 radiolabelled" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0372 name: subcellular preparation namespace: PSI-MI def: "Cell lysates are partially fractionated to isolate a specific subcellular fraction." [PMID:14755292] subset: PSI-MI_slim synonym: "subcellular prep" EXACT PSI-MI-short [] is_a: MI:0344 ! cell lysate [Term] id: MI:0373 name: dye label namespace: PSI-MI def: "Dye coupled to a molecule allowing its identification isolation and monitoring." [PMID:14577292] subset: PSI-MI_slim synonym: "dye labelled" EXACT PSI-MI-short [] is_a: MI:0505 ! experimental feature [Term] id: MI:0374 name: cyanine label namespace: PSI-MI def: "The organic cyanine dyes emit in the red range (>550 nm), offer a number of advantages. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids." [PMID:14577292] subset: PSI-MI_slim is_a: MI:0373 ! dye label is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0375 name: cy3 label namespace: PSI-MI def: "The organic cyanine Cy3 emits maximally at 570 nm." [PMID:14577292] subset: PSI-MI_slim is_a: MI:0374 ! cyanine label [Term] id: MI:0376 name: cy5 label namespace: PSI-MI def: "The organic cyanine Cy5 emits maximally at 670 nm." [PMID:14577292] subset: PSI-MI_slim is_a: MI:0374 ! cyanine label [Term] id: MI:0377 name: fluorescein isothiocyanate label namespace: PSI-MI def: "Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm." [PMID:14577292] subset: PSI-MI_slim synonym: "FITC labelled" EXACT PSI-MI-alternate [] synonym: "fitc labelled" EXACT PSI-MI-short [] synonym: "fluorescein isothiocyanate labbeled" EXACT PSI-MI-alternate [] is_a: MI:0373 ! dye label is_a: MI:0939 ! fluorescein label [Term] id: MI:0378 name: rare isotope label namespace: PSI-MI def: "Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." [PMID:14577292] subset: PSI-MI_slim synonym: "rare isotope label" EXACT PSI-MI-short [] is_a: MI:0253 ! isotope label [Term] id: MI:0379 name: 13c label namespace: PSI-MI def: "Molecules labelled with isotope 13 of carbon atoms." [PMID:14577292] subset: PSI-MI_slim synonym: "13C" EXACT PSI-MI-alternate [] synonym: "C13" EXACT PSI-MI-alternate [] is_a: MI:0378 ! rare isotope label [Term] id: MI:0380 name: 15n label namespace: PSI-MI def: "Molecules labelled with isotope 15 of nytrogen atoms." [PMID:14577292] subset: PSI-MI_slim synonym: "15N" EXACT PSI-MI-alternate [] synonym: "N15" EXACT PSI-MI-alternate [] is_a: MI:0378 ! rare isotope label [Term] id: MI:0381 name: 2h label namespace: PSI-MI def: "Molecules labelled with isotope 2 of hydrogen atoms." [PMID:14577292] subset: PSI-MI_slim synonym: "2H2" EXACT PSI-MI-alternate [] synonym: "D2" EXACT PSI-MI-alternate [] synonym: "deuterium" EXACT PSI-MI-alternate [] is_a: MI:0378 ! rare isotope label [Term] id: MI:0382 name: mutation increasing interaction namespace: PSI-MI def: "Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction)." [PMID:14577292] subset: PSI-MI_slim synonym: "mutation increasing" EXACT PSI-MI-short [] is_a: MI:0118 ! mutation [Term] id: MI:0383 name: biopolymer namespace: PSI-MI def: "Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds." [PMID:14577292] subset: PSI-MI_slim is_a: MI:0313 ! interactor type [Term] id: MI:0384 name: alexa label namespace: PSI-MI def: "All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm)." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0373 ! dye label is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0385 name: alexa 350 label namespace: PSI-MI def: "Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0386 name: alexa 430 label namespace: PSI-MI def: "Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0387 name: alexa 488 label namespace: PSI-MI def: "Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0388 name: alexa 532 label namespace: PSI-MI def: "Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0389 name: alexa 546 label namespace: PSI-MI def: "Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0390 name: alexa 568 label namespace: PSI-MI def: "Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0391 name: alexa 594 label namespace: PSI-MI def: "Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm." [PMID:10449539] subset: PSI-MI_slim is_a: MI:0384 ! alexa label [Term] id: MI:0396 name: predetermined participant namespace: PSI-MI def: "Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s)." [PMID:14755292] subset: PSI-MI_slim synonym: "predetermined" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0397 name: two hybrid array namespace: PSI-MI def: "Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames." [PMID:11827624, PMID for application instance:10688190] subset: PSI-MI_slim is_a: MI:0018 ! two hybrid [Term] id: MI:0398 name: two hybrid pooling approach namespace: PSI-MI def: "In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results." [PMID:11283351, PMID:20946815] subset: PSI-MI_slim synonym: "two hybrid pooling" EXACT PSI-MI-short [] is_a: MI:0018 ! two hybrid [Term] id: MI:0399 name: two hybrid fragment pooling approach namespace: PSI-MI def: "Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen." [PMID:12634794] subset: PSI-MI_slim synonym: "2h fragment pooling" EXACT PSI-MI-short [] is_a: MI:1112 ! two hybrid prey pooling approach [Term] id: MI:0400 name: affinity technology namespace: PSI-MI def: "Techniques which depend upon the strength of the interaction between two entities." [PMID:14755292] subset: PSI-MI_slim synonym: "affinity techniques" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical [Term] id: MI:0401 name: biochemical namespace: PSI-MI def: "The application of chemical principles and methods to biological experiments to demonstrate an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0402 name: chromatin immunoprecipitation assay namespace: PSI-MI def: "Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques" [PMID:12054902] subset: PSI-MI_slim synonym: "ch-ip" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation [Term] id: MI:0403 name: colocalization namespace: PSI-MI def: "Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0190 ! interaction type [Term] id: MI:0404 name: comigration in non denaturing gel electrophoresis namespace: PSI-MI def: "comigration by non denaturing gel electrophoresis." [PMID:14755292] subset: PSI-MI_slim synonym: "comig non denat gel" EXACT PSI-MI-short [] is_a: MI:0807 ! comigration in gel electrophoresis [Term] id: MI:0405 name: competition binding namespace: PSI-MI def: "Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0406 name: deacetylase assay namespace: PSI-MI def: "Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study [Term] id: MI:0407 name: direct interaction namespace: PSI-MI def: "Interaction that is proven to involve only its interactors." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0915 ! physical association [Term] id: MI:0408 name: disulfide bond namespace: PSI-MI def: "Covalent bond mediated by 2 sulfur atoms." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0195 ! covalent binding [Term] id: MI:0409 name: dna footprinting namespace: PSI-MI def: "Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding.\nOBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA' \nreplace by:MI:0417" [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0410 name: electron tomography namespace: PSI-MI def: "Electron tomography is a general method for three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images (i.e. from a tilt series) recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution." [PMID:12160704] subset: PSI-MI_slim synonym: "electron tomog" EXACT PSI-MI-short [] is_a: MI:0040 ! electron microscopy [Term] id: MI:0411 name: enzyme linked immunosorbent assay namespace: PSI-MI def: "Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein)." [PMID:11906746] subset: PSI-MI_slim synonym: "ELISA" EXACT PSI-MI-alternate [] synonym: "elisa" EXACT PSI-MI-short [] is_a: MI:0421 ! identification by antibody is_a: MI:0892 ! solid phase assay [Term] id: MI:0412 name: electrophoretic mobility supershift assay namespace: PSI-MI def: "The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified." [PMID:12169687] subset: PSI-MI_slim synonym: "emsa supershift" EXACT PSI-MI-short [] is_a: MI:0413 ! electrophoretic mobility shift assay [Term] id: MI:0413 name: electrophoretic mobility shift assay namespace: PSI-MI def: "This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a radiolabeled nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). After the electrophoresis run and autoradiography by comparing the nucleic acid migration in the two lanes the retardation of the nucleic acid due to its interaction with a protein can be easily observed." [PMID:12169687] subset: PSI-MI_slim synonym: "band shift" EXACT PSI-MI-alternate [] synonym: "emsa" EXACT PSI-MI-short [] synonym: "Gel retardation assay" EXACT PSI-MI-alternate [] is_a: MI:0807 ! comigration in gel electrophoresis is_a: MI:0892 ! solid phase assay [Term] id: MI:0414 name: enzymatic reaction namespace: PSI-MI def: "terms aiming to represent biochemical reactions referring to their resulting product modifications." [PMID:14755292] subset: PSI-MI_slim synonym: "Biochemical reaction" EXACT PSI-MI-alternate [] is_a: MI:0407 ! direct interaction [Term] id: MI:0415 name: enzymatic study namespace: PSI-MI def: "Participants are enzyme or substrate in a biochemical reaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0401 ! biochemical [Term] id: MI:0416 name: fluorescence microscopy namespace: PSI-MI def: "Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescence imaging" EXACT PSI-MI-short [] is_a: MI:0428 ! imaging technique [Term] id: MI:0417 name: footprinting namespace: PSI-MI def: "footprinting analysis is used to identify regions of molecules directly involved in binding other macromolecules and therefore protected from the effects of degradative enzymes." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0401 ! biochemical [Term] id: MI:0418 name: genetic namespace: PSI-MI def: "methods supporting genetic interactions.\nOBSOLETE as too unspecific use Genetic interference instead MI:0254." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0419 name: gtpase assay namespace: PSI-MI def: "Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate." [PMID:14755292] subset: PSI-MI_slim synonym: "gtp hydrolisis" EXACT PSI-MI-alternate [] synonym: "GTPase" EXACT PSI-MI-alternate [] is_a: MI:0879 ! nucleoside triphosphatase assay [Term] id: MI:0420 name: kinase homogeneous time resolved fluorescence namespace: PSI-MI def: "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase." [PMID:14987100] subset: PSI-MI_slim synonym: "homogeneous time-resolved fluorescence" EXACT PSI-MI-alternate [] synonym: "kinase HTRF" EXACT PSI-MI-alternate [] synonym: "kinase htrf" EXACT PSI-MI-short [] is_a: MI:0424 ! protein kinase assay is_a: MI:0510 ! homogeneous time resolved fluorescence [Term] id: MI:0421 name: identification by antibody namespace: PSI-MI def: "Antibody mediated participant identification." [PMID:14755292] subset: PSI-MI_slim synonym: "antibody detection" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0422 name: immunostaining namespace: PSI-MI def: "Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0421 ! identification by antibody [Term] id: MI:0423 name: in-gel kinase assay namespace: PSI-MI def: "Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography." [PMID:14755292] subset: PSI-MI_slim synonym: "in gel kinase assay" EXACT PSI-MI-short [] is_a: MI:0424 ! protein kinase assay [Term] id: MI:0424 name: protein kinase assay namespace: PSI-MI def: "Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0841 ! phosphotransferase assay [Term] id: MI:0425 name: kinase scintillation proximity assay namespace: PSI-MI def: "Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate." [PMID:14755292] subset: PSI-MI_slim synonym: "kinase spa" EXACT PSI-MI-short [] is_a: MI:0099 ! scintillation proximity assay is_a: MI:0424 ! protein kinase assay [Term] id: MI:0426 name: light microscopy namespace: PSI-MI def: "Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0428 ! imaging technique [Term] id: MI:0427 name: Identification by mass spectrometry namespace: PSI-MI def: "identification by mass spectrometry." [PMID:14755292] subset: PSI-MI_slim synonym: "ms participant" EXACT PSI-MI-short [] is_a: MI:0661 ! experimental participant identification [Term] id: MI:0428 name: imaging technique namespace: PSI-MI def: "Methods that provide images of molecules at various resolution depending on the technology used." [PMID:14755292] subset: PSI-MI_slim synonym: "microscopy" EXACT PSI-MI-alternate [] is_a: MI:0045 ! experimental interaction detection [Term] id: MI:0429 name: necessary binding region namespace: PSI-MI def: "A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner." [PMID:14755292] subset: PSI-MI_slim synonym: "deletion disrupting interaction" EXACT [] synonym: "necessary binding site" EXACT [] synonym: "required to bind" EXACT PSI-MI-short [] is_a: MI:0117 ! binding-associated region is_a: MI:0573 ! mutation disrupting interaction is_a: MI:1128 ! mutation disrupting interaction strength is_a: MI:1129 ! mutation disrupting interaction rate [Term] id: MI:0430 name: nucleic acid uv cross-linking assay namespace: PSI-MI def: "Radiolabelled nucleic acids with a known sequence are incubated with purified proteins or reproducible protein mixture (HPLC eluate fractions) and then irradiated with UV. The complex are treated with an enzyme to remove the unbound nucleic acid (Rnase A or Dnase I for example), washed and then analyzed by electrophoresis. The eventual complexes are identified by autoradiography. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it. The affinity of the binding can be estimated by adding a non-labelled nucleic acid as competitor before the UV irradiation." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl ac uv crosslink" EXACT PSI-MI-short [] is_a: MI:0030 ! cross-linking study [Term] id: MI:0431 name: obsolete namespace: PSI-MI def: "Deprecated terms.\nOBSOLETE term replaced by the default OBO class 'Obsolete'." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0432 name: one hybrid namespace: PSI-MI def: "Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors." [PMID:10589421] subset: PSI-MI_slim synonym: "one-hybrid" EXACT PSI-MI-alternate [] synonym: "yeast one hybrid" EXACT PSI-MI-alternate [] synonym: "yeast one-hybrid" EXACT PSI-MI-alternate [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0433 name: partial identification of protein sequence namespace: PSI-MI def: "partial protein sequence identification." [PMID:14755292] subset: PSI-MI_slim synonym: "partial id prot seq" EXACT PSI-MI-short [] is_a: MI:0093 ! protein sequence identification [Term] id: MI:0434 name: phosphatase assay namespace: PSI-MI def: "Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study [Term] id: MI:0435 name: protease assay namespace: PSI-MI def: "Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0990 ! cleavage assay [Term] id: MI:0436 name: protein footprinting namespace: PSI-MI def: "Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site." [PMID:14600024, PMID:14967031, PMID:14987073] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection [Term] id: MI:0437 name: protein three hybrid namespace: PSI-MI def: "Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected." [PMID:12052864, PMID:12761205, PMID:12935900] subset: PSI-MI_slim synonym: "bridge assay" EXACT PSI-MI-alternate [] synonym: "protein 3-hybrid" EXACT PSI-MI-alternate [] synonym: "protein tri hybrid" EXACT PSI-MI-alternate [] synonym: "trihybrid" EXACT PSI-MI-alternate [] is_a: MI:0018 ! two hybrid is_a: MI:0588 ! three hybrid [Term] id: MI:0438 name: rna three hybrid namespace: PSI-MI def: "In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated." [PMID:12162957, PMID:8972875] subset: PSI-MI_slim synonym: "rna 3-hybrid" EXACT PSI-MI-alternate [] synonym: "rna tri hybrid" EXACT PSI-MI-alternate [] synonym: "rna-three hybrid" EXACT PSI-MI-alternate [] synonym: "Three hybrid system" EXACT PSI-MI-alternate [] is_a: MI:0588 ! three hybrid [Term] id: MI:0439 name: random spore analysis namespace: PSI-MI def: "A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability." [PMID:14755292] subset: PSI-MI_slim synonym: "random-spore analysis" EXACT PSI-MI-alternate [] synonym: "RSA" EXACT PSI-MI-alternate [] synonym: "rsa" EXACT PSI-MI-short [] synonym: "spore germination" EXACT PSI-MI-alternate [] is_a: MI:0254 ! genetic interference [Term] id: MI:0440 name: saturation binding namespace: PSI-MI def: "Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0441 name: synthetic genetic analysis namespace: PSI-MI def: "Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation." [PMID:14755292] subset: PSI-MI_slim synonym: "SGA" EXACT PSI-MI-alternate [] synonym: "sga" EXACT PSI-MI-short [] is_a: MI:0254 ! genetic interference [Term] id: MI:0442 name: sufficient binding region namespace: PSI-MI def: "Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer." [PMID:14755292] subset: PSI-MI_slim synonym: "sufficient binding site" EXACT [] synonym: "sufficient to bind" EXACT PSI-MI-short [] is_a: MI:0117 ! binding-associated region [Term] id: MI:0443 name: ubiquitin binding namespace: PSI-MI def: "Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner.\nOBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0444 name: database citation namespace: PSI-MI def: "Database citation list names of databases commonly used to cross reference interaction data." [PMID:14755292] subset: Drugable subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0445 name: literature database namespace: PSI-MI def: "Databases acting as a source of literature information." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "experiment xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation [Term] id: MI:0446 name: pubmed namespace: PSI-MI def: "PubMed is designed to provide access to citations from biomedical literature.\nhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi" [PMID:14755292] subset: Drugable subset: PSI-MI_slim xref: id-validation-regexp:\"[0-9\]+\" xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=${ac}&dopt=Abstract" is_a: MI:0445 ! literature database [Term] id: MI:0447 name: feature database namespace: PSI-MI def: "A database describing a feature on a molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "feature xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation [Term] id: MI:0448 name: gene ontology namespace: PSI-MI def: "The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.\nhttp://www.ebi.ac.uk/GO" [PMID:14755292] subset: PSI-MI_slim synonym: "go" EXACT PSI-MI-short [] xref: id-validation-regexp:\"GO\:[0-9\]\{7}\" is_a: MI:0447 ! feature database is_a: MI:0461 ! interaction database [Term] id: MI:0449 name: interpro namespace: PSI-MI def: "InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences.\nhttp://www.ebi.ac.uk/interpro/" [PMID:1252001] subset: PSI-MI_slim synonym: "InterPro" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"IPR[0-9\]\{6}\" xref: search-url: "http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=${ac}" is_a: MI:0447 ! feature database [Term] id: MI:0450 name: cdd namespace: PSI-MI def: "The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence.\nhttp://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml" [PMID:14755292] subset: PSI-MI_slim synonym: "CDD" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\]+\" is_a: MI:0447 ! feature database [Term] id: MI:0451 name: pfam namespace: PSI-MI def: "Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.\nhttp://www.sanger.ac.uk/Software/Pfam" [PMID:14755292] subset: PSI-MI_slim synonym: "Pfam" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"PF[0-9\]\{5}\" is_a: MI:0449 ! interpro [Term] id: MI:0452 name: pirsf namespace: PSI-MI def: "PIRSF is a classification system based on evolutionary relationship of whole proteins.\nhttp://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml" [PMID:14755292] subset: PSI-MI_slim synonym: "PIRSF" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"PIRSF[0-9\]\{5}\" is_a: MI:0449 ! interpro [Term] id: MI:0453 name: prints namespace: PSI-MI def: "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family.\nhttp://umber.sbs.man.ac.uk/dbbrowser/PRINTS/" [PMID:14755292] subset: PSI-MI_slim synonym: "PRINTS" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"PR[0-9\]\{6}\" is_a: MI:0449 ! interpro [Term] id: MI:0454 name: prodom namespace: PSI-MI def: "The ProDom protein domain database consists of an automatic compilation of homologous domains.\nhttp://protein.toulouse.inra.fr/prodom.html" [PMID:14755292] subset: PSI-MI_slim synonym: "ProDom" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"PD[0-9\]\{6}\" is_a: MI:0449 ! interpro [Term] id: MI:0455 name: prosite namespace: PSI-MI def: "PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles.\nhttp://us.expasy.org/prosite/" [PMID:14755292] subset: PSI-MI_slim synonym: "Prosite" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"PS[0-9\]\{5}\" is_a: MI:0449 ! interpro [Term] id: MI:0456 name: scop superfamily namespace: PSI-MI def: "SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain.\nhttp://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/" [PMID:14755292] subset: PSI-MI_slim synonym: "SCOP superfamily" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\]+\" is_a: MI:0449 ! interpro [Term] id: MI:0457 name: smart namespace: PSI-MI def: "SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures.\nhttp://smart.embl-heidelberg.de/" [PMID:14755292] subset: PSI-MI_slim synonym: "SMART" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"SM[0-9\]\{5}\" is_a: MI:0449 ! interpro [Term] id: MI:0458 name: tigrfams namespace: PSI-MI def: "TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation.\nhttp://www.tigr.org/TIGRFAMs" [PMID:14755292] subset: PSI-MI_slim synonym: "TIGRFAMs" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"TIGR[0-9\]+\" is_a: MI:0449 ! interpro [Term] id: MI:0459 name: mmdb namespace: PSI-MI def: "MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank.\nhttp://www.ncbi.nlm.nih.gov/Structure" [PMID:14755292] subset: PSI-MI_slim synonym: "MMDB" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\]+\" is_a: MI:0447 ! feature database is_a: MI:0461 ! interaction database [Term] id: MI:0460 name: rcsb pdb namespace: PSI-MI def: "The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. \nhttp://www.pdb.org/" [PMID:14634627] subset: Drugable subset: PSI-MI_slim synonym: "PDB" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\" xref: search-url: "http://www.pdb.org/pdb/explore/explore.do?structureId=${ac}" is_a: MI:0805 ! wwpdb [Term] id: MI:0461 name: interaction database namespace: PSI-MI def: "Databases that contain experimental or predictive molecular interaction data." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "interaction xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation [Term] id: MI:0462 name: bind namespace: PSI-MI def: "The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions.\nhttp://www.blueprint.org/bind" [PMID:14755292] subset: PSI-MI_slim synonym: "BIND" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\]+\" is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0463 name: biogrid namespace: PSI-MI def: "The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions.\nhttp://thebiogrid.org" [PMID:21071413] subset: PSI-MI_slim synonym: "BioGRID" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0464 name: cygd namespace: PSI-MI def: "The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.\nhttp://mips.gsf.de/proj/yeast/CYGD.\nhttp://mips.gsf.de/genre/proj/mpact" [PMID:14755292] subset: PSI-MI_slim synonym: "CYGD" EXACT PSI-MI-alternate [] synonym: "CYGD (MIPS)" EXACT PSI-MI-alternate [] synonym: "MIPS" EXACT PSI-MI-alternate [] synonym: "MPact" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\]+|[A-Z\]\{3}[0-9\]\{3}[A-Za-z\](-[A-Za-z\])?|[A-Z0-9\]+\\.[0-9\]+|YM[A-Z\][0-9\]\{3}[a-z\][0-9\]\" is_a: MI:0489 ! source database is_a: MI:1094 ! genome databases is_a: MI:1106 ! pathways database [Term] id: MI:0465 name: dip namespace: PSI-MI def: "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.\nhttp://dip.doe-mbi.ucla.edu/" [PMID:14755292] subset: PSI-MI_slim synonym: "DIP" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"DIP[0-9\]+[NE\]\" is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database is_a: MI:0973 ! imex source [Term] id: MI:0466 name: ecocyc namespace: PSI-MI def: "EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655.\nhttp://ecocyc.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "EcoCyc" EXACT PSI-MI-alternate [] is_a: MI:1106 ! pathways database [Term] id: MI:0467 name: reactome namespace: PSI-MI def: "The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.\nhttp://www.reactome.org/" [PMID:21067998] subset: PSI-MI_slim synonym: "Genome Knowledge Base" EXACT PSI-MI-alternate [] synonym: "GKB" EXACT PSI-MI-alternate [] synonym: "Reactome" EXACT PSI-MI-alternate [] is_a: MI:1106 ! pathways database [Term] id: MI:0468 name: hprd namespace: PSI-MI def: "The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.\nhttp://www.hprd.org/" [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "HPRD" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database [Term] id: MI:0469 name: intact namespace: PSI-MI def: "INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of protein interactions.\nhttp://www.ebi.ac.uk/intact" [PMID:14681455, PMID:19850723, PMID:22121220] subset: PSI-MI_slim synonym: "IntAct" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"EBI-[0-9\]+|IA\:[0-9\]+\" xref: search-url: "http://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=${ac}" is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database is_a: MI:0973 ! imex source [Term] id: MI:0470 name: kegg namespace: PSI-MI def: "KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions.\nhttp://www.genome.ad.jp/kegg/" [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "KEGG" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[a-zA-Z\]+\:[a-zA-Z\]+[0-9\]+\" is_a: MI:0473 ! participant database is_a: MI:1106 ! pathways database [Term] id: MI:0471 name: mint namespace: PSI-MI def: "The Moleculer INTeraction database (MINT) is a relational database designed to store interactions between biological molecules.\nhttp://mint.bio.uniroma2.it/mint/" [PMID:14755292] subset: PSI-MI_slim synonym: "MINT" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"MINT_[0-9\]+\" is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database is_a: MI:0973 ! imex source [Term] id: MI:0472 name: pdbe namespace: PSI-MI def: "The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB).\nhttp://www.ebi.ac.uk/pdbe/" [PMID:16381867] subset: PSI-MI_slim synonym: "" RELATED [] synonym: "e-MSD" EXACT [] synonym: "MSD" RELATED [] synonym: "PQS" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\" xref: search-url: "http://www.ebi.ac.uk/pdbe-srv/atlas?id=${ac}" is_a: MI:0805 ! wwpdb [Term] id: MI:0473 name: participant database namespace: PSI-MI def: "Database of molecules participating in molecular interactions." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "participant xref" EXACT PSI-MI-short [] is_a: MI:0444 ! database citation [Term] id: MI:0474 name: chebi namespace: PSI-MI def: "A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI).\nhttp://www.ebi.ac.uk/chebi/" [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "ChEBI" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"CHEBI\:[0-9\]+\" xref: search-url: "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=${ac}" is_a: MI:2054 ! bioactive entity reference [Term] id: MI:0475 name: ddbj/embl/genbank namespace: PSI-MI def: "DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation.\nhttp://www.ebi.ac.uk/embl/Contact/collaboration" [PMID:14755292] subset: PSI-MI_slim synonym: "DDBJ" EXACT PSI-MI-alternate [] synonym: "DDBJ/EMBL/GenBank" EXACT PSI-MI-alternate [] synonym: "EMBL" EXACT PSI-MI-alternate [] synonym: "GenBank" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[A-Z\][0-9\]\{5}|[A-Z\][0-9\]\{5}\\.[0-9\]+|[A-Z\]\{2}[0-9\]\{6}|[A-Z\]\{2}[0-9\]\{6}\\.[0-9\]+|[A-Z\]\{4}[0-9\]\{8}|[A-Z\]\{4}[0-9\]\{8}\\.[0-9\]+\" xref: search-url: "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBLSVA&id=${ac}" is_a: MI:0683 ! sequence database [Term] id: MI:0476 name: ensembl namespace: PSI-MI def: "Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes.\nhttp://www.ensembl.org" [PMID:15078858] subset: PSI-MI_slim synonym: "Ensembl" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"ENS[A-Z\]+[0-9\]\{11}|[A-Z\]\{3}[0-9\]\{3}[A-Za-z\](-[A-Za-z\])?|CG[0-9\]+|[A-Z0-9\]+\\.[0-9\]+|YM[A-Z\][0-9\]\{3}[a-z\][0-9\]\" is_a: MI:1094 ! genome databases [Term] id: MI:0477 name: entrez gene/locuslink namespace: PSI-MI def: "LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci.\nhttp://www.ncbi.nlm.nih.gov/LocusLink/" [PMID:14755292] subset: PSI-MI_slim synonym: "Entrez gene/locuslink" EXACT PSI-MI-alternate [] synonym: "entrezgene/locuslink" EXACT PSI-MI-short [] xref: id-validation-regexp:\"[0-9\]+|[A-Z\]\{1\,2}_[0-9\]+|[A-Z\]\{1\,2}_[A-Z\]\{1\,4}[0-9\]+\" is_a: MI:1109 ! gene database [Term] id: MI:0478 name: flybase namespace: PSI-MI def: "FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila.\nhttp://fbserver.gen.cam.ac.uk:7081/" [PMID:14755292] subset: PSI-MI_slim synonym: "FlyBase" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"FBgn[0-9\]\{7}\" xref: search-url: "http://flybase.net/cgi-bin/fbannq.html?acc=${ac}" is_a: MI:1094 ! genome databases [Term] id: MI:0479 name: mgd/mgi namespace: PSI-MI def: "Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.\nhttp://www.informatics.jax.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "MGD/MGI" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"MGI\:[0-9\]+\" is_a: MI:1094 ! genome databases [Term] id: MI:0480 name: omim namespace: PSI-MI def: "Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases.\nhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM" [PMID:14755292] subset: PSI-MI_slim synonym: "OMIM" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\]+\" xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=${ac}" is_a: MI:0683 ! sequence database [Term] id: MI:0481 name: refseq namespace: PSI-MI def: "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms.\nhttp://www.ncbi.nlm.nih.gov/RefSeq/" [PMID:14755292] subset: PSI-MI_slim synonym: "Refseq" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[XNZ\][A-Z\]_[0-9\]+|[0-9\]+|[XNZ\][A-Z\]_[0-9\]+\\.[0-9\]+\" is_a: MI:1096 ! protein sequence databases [Term] id: MI:0482 name: rfam namespace: PSI-MI def: "Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families.\nhttp://www.sanger.ac.uk/Software/Rfam/" [PMID:14755292] subset: PSI-MI_slim synonym: "rfam" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"RF[0-9\]\{5}\" is_a: MI:0683 ! sequence database [Term] id: MI:0483 name: rgd namespace: PSI-MI def: "The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data.\nhttp://rgd.mcw.edu/" [PMID:14755292] subset: PSI-MI_slim synonym: "RGD" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\]+\" is_a: MI:1094 ! genome databases [Term] id: MI:0484 name: sgd namespace: PSI-MI def: "SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.\nhttp://www.yeastgenome.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "SGD" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"S[0-9\]\{9}\" xref: search-url: "http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=${ac}" is_a: MI:1094 ! genome databases [Term] id: MI:0485 name: uniparc namespace: PSI-MI def: "UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources.\nhttp://www.ebi.ac.uk/uniparc/" [PMID:14681372] subset: PSI-MI_slim synonym: "UniParc" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"UPI[A-F0-9\]\{10}\" xref: search-url: "http://www.ebi.uniprot.org/entry/${ac}" is_a: MI:1097 ! uniprot [Term] id: MI:0486 name: uniprot knowledge base namespace: PSI-MI def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.\nhttp://www.uniprot.org" [PMID:14681372] subset: PSI-MI_slim synonym: "uniprotkb" EXACT PSI-MI-short [] synonym: "UniProtKB" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]|[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]-[0-9\]+|[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]-PRO_[0-9\]\{10}\" xref: search-url: "http://www.uniprot.org/uniprot/{ac}" is_a: MI:1097 ! uniprot [Term] id: MI:0487 name: wormbase namespace: PSI-MI def: "WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser.\nhttp://www.wormbase.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "WormBase" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"WBGene[0-9\]\{8}\" is_a: MI:1094 ! genome databases [Term] id: MI:0488 name: psi-mi namespace: PSI-MI def: "PSI-MI." [PMID:14755292] subset: PSI-MI_slim synonym: "PSI-MI" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"MI\:[0-9\]\{4}\" xref: search-url: "http://www.ebi.ac.uk/ontology-lookup/?termId=${ac}" is_a: MI:0444 ! database citation [Term] id: MI:0489 name: source database namespace: PSI-MI def: "Database that originally provided the interaction record for exchange purposes." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0444 ! database citation [Term] id: MI:0490 name: experiment condition namespace: PSI-MI def: "Describes the location of the experiment.\nOBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0491 name: in silico namespace: PSI-MI def: "Results generated by predictive bioinformatics approaches rather than experimental data.\nOBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "Predictive" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0492 name: in vitro namespace: PSI-MI def: "Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins.\nOBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0493 name: in vivo namespace: PSI-MI def: "Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study.\nOBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0494 name: in situ namespace: PSI-MI def: "Literally, in place i.e. the protein is in its natural environment during the experiment.\nOBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0495 name: experimental role namespace: PSI-MI def: "Role played by the participant within the experiment." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0496 name: bait namespace: PSI-MI def: "Molecule experimentally treated to capture its interacting partners." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0497 name: neutral component namespace: PSI-MI def: "Molecule role in an experimental setting that does not have an embedded asymmetry." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0498 name: prey namespace: PSI-MI def: "Molecule experimentally identified as being captured by a given bait." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0499 name: unspecified role namespace: PSI-MI def: "Role not specified or not applicable to the data." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role is_a: MI:0500 ! biological role [Term] id: MI:0500 name: biological role namespace: PSI-MI def: "Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0501 name: enzyme namespace: PSI-MI def: "Molecule catalyzing a modification on its interacting partner." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0500 ! biological role [Term] id: MI:0502 name: enzyme target namespace: PSI-MI def: "Molecule that is the target of its binding partner catalytic activity." [PMID:14755292] subset: PSI-MI_slim synonym: "substrate" EXACT PSI-MI-alternate [] is_a: MI:0500 ! biological role [Term] id: MI:0503 name: self namespace: PSI-MI def: "Molecule that makes intramolecular interactions." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role is_a: MI:0500 ! biological role [Term] id: MI:0505 name: experimental feature namespace: PSI-MI def: "The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0116 ! feature type [Term] id: MI:0506 name: over expressed level namespace: PSI-MI def: "A molecule is estimated to be expressed at higher levels than in physiological condition." [PMID:14755292] subset: PSI-MI_slim synonym: "over-expressed" EXACT PSI-MI-short [] is_a: MI:0221 ! expression level is_a: MI:0803 ! expression level alteration [Term] id: MI:0507 name: tag namespace: PSI-MI def: "Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labelled molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0508 name: deacetylase radiometric assay namespace: PSI-MI def: "Measures the release of radiolabelled acetic acid from a pre-labeled molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "radiolabeled acetate" EXACT PSI-MI-short [] is_a: MI:0406 ! deacetylase assay [Term] id: MI:0509 name: phosphatase homogeneous time resolved fluorescence namespace: PSI-MI def: "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase." [PMID:14987100] subset: PSI-MI_slim synonym: "homogeneous time-resolved fluorescence" EXACT PSI-MI-alternate [] synonym: "phosphatase HTRF" EXACT PSI-MI-alternate [] synonym: "phosphatase htrf" EXACT PSI-MI-short [] is_a: MI:0434 ! phosphatase assay is_a: MI:0510 ! homogeneous time resolved fluorescence [Term] id: MI:0510 name: homogeneous time resolved fluorescence namespace: PSI-MI def: "Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates." [PMID:14987100] subset: PSI-MI_slim synonym: "homogeneous time-resolved fluorescence" EXACT PSI-MI-alternate [] synonym: "htrf" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology [Term] id: MI:0511 name: protease homogeneous time resolved fluorescence namespace: PSI-MI def: "Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease." [PMID:14987100] subset: PSI-MI_slim synonym: "Protease HTRF" EXACT PSI-MI-alternate [] synonym: "protease htrf" EXACT PSI-MI-short [] is_a: MI:0435 ! protease assay is_a: MI:0510 ! homogeneous time resolved fluorescence [Term] id: MI:0512 name: zymography namespace: PSI-MI def: "Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity." [PMID:2071592] subset: PSI-MI_slim is_a: MI:0435 ! protease assay [Term] id: MI:0513 name: collagen film assay namespace: PSI-MI def: "Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen." [PMID:6247938] subset: PSI-MI_slim is_a: MI:0435 ! protease assay [Term] id: MI:0514 name: in gel phosphatase assay namespace: PSI-MI def: "Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography." [PMID:14755292] subset: PSI-MI_slim synonym: "in gel phosphatase" EXACT PSI-MI-short [] is_a: MI:0434 ! phosphatase assay [Term] id: MI:0515 name: methyltransferase assay namespace: PSI-MI def: "Measures the catalysis of the transfer of a methyl group to an acceptor molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "methyltransferase as" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study [Term] id: MI:0516 name: methyltransferase radiometric assay namespace: PSI-MI def: "Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor." [PMID:14755292] subset: PSI-MI_slim synonym: "radiolabeled methyl" EXACT PSI-MI-short [] is_a: MI:0515 ! methyltransferase assay [Term] id: MI:0517 name: radiolabel namespace: PSI-MI def: "A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "radiolabeled" EXACT PSI-MI-alternate [] synonym: "radiolabelled" EXACT PSI-MI-short [] is_a: MI:0253 ! isotope label [Term] id: MI:0518 name: flag tag namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." [PMID:14755292] subset: PSI-MI_slim synonym: "DYKDDDDKV epitope tag" EXACT PSI-MI-alternate [] synonym: "FLAG" EXACT PSI-MI-alternate [] synonym: "FLAG-tagged" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0519 name: glutathione s tranferase tag namespace: PSI-MI def: "The protein is expressed and purified as a fusion to the glutathione S-tranferase protein." [PMID:14755292] subset: PSI-MI_slim synonym: "glutathione S-tranferase tag" EXACT PSI-MI-alternate [] synonym: "gst tag" EXACT PSI-MI-short [] is_a: MI:0365 ! enzyme tag [Term] id: MI:0520 name: ha tag namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available." [PMID:14755292] subset: PSI-MI_slim synonym: "YPYDVPDYA epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0521 name: his tag namespace: PSI-MI def: "The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies." [PMID:14755292] subset: PSI-MI_slim synonym: "6-His-tag" EXACT PSI-MI-alternate [] synonym: "Hexa-His-tag" EXACT PSI-MI-alternate [] synonym: "Histidine-tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0522 name: myc tag namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." [PMID:14755292] subset: PSI-MI_slim synonym: "EUKLISEED epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0523 name: t7 tag namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available." [PMID:14755292] subset: PSI-MI_slim synonym: "MASMTGGQQMG epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0524 name: calmodulin binding peptide plus protein a tag namespace: PSI-MI def: "Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This tag allows two steps purification steps ensuring a highly selective purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag)." [PMID:14755292] subset: PSI-MI_slim synonym: "CBP-ProtA tagged" EXACT PSI-MI-alternate [] synonym: "tap tagged" EXACT PSI-MI-short [] is_a: MI:0677 ! tandem tag [Term] id: MI:0525 name: v5 tag namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available." [PMID:14755292] subset: PSI-MI_slim synonym: "GKPIPNPLLGLDST epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0526 name: n-acetyl-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00723." [PMID:14755292, RESID:AA0048, RESID:AA0055] synonym: "acetyllysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0527 name: adp ribosylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00752." [PMID:14755292] synonym: "adp-ribosylated" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0528 name: omega-n-(adp-ribosyl)-arginine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00177." [PMID:14755292, RESID:AA0168] synonym: "(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid" EXACT PSI-MI-alternate [] synonym: "adp-ribosylarginine" EXACT PSI-MI-short [] synonym: "N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine" EXACT PSI-MI-alternate [] synonym: "N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] synonym: "omega-N-(ADP-ribosyl)-L-arginine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0529 name: s-(adp-ribosyl)-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00178." [PMID:14755292, RESID:AA0169] synonym: "(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "adp-ribosylcysteine" EXACT PSI-MI-short [] synonym: "S-(ADP-ribosyl)-L-cysteine" EXACT PSI-MI-alternate [] synonym: "S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] synonym: "S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0530 name: glutamyl-5-poly(adp-ribose) namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00300." [PMID:14755292, RESID:AA0295] synonym: "(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid" EXACT PSI-MI-alternate [] synonym: "adp-ribosylglutamate" EXACT PSI-MI-short [] synonym: "L-glutamyl-5-poly(ADP-ribose)" EXACT PSI-MI-alternate [] synonym: "L-isoglutamyl-poly(ADP-ribose)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0531 name: o-(adp-ribosyl)-serine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00242." [PMID:14755292, RESID:AA0237] synonym: "(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula" EXACT PSI-MI-alternate [] synonym: "adp-ribosylserine" EXACT PSI-MI-short [] synonym: "O-(ADP-ribosyl)-L-serine" EXACT PSI-MI-alternate [] synonym: "O3-(ADP-ribosyl)-L-serine" EXACT PSI-MI-alternate [] synonym: "O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine" EXACT PSI-MI-alternate [] synonym: "O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0532 name: n4-(adp-ribosyl)-asparagine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00236." [PMID:14755292, RESID:AA0231] synonym: "(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid" EXACT PSI-MI-alternate [] synonym: "adpribosylasparagine" EXACT PSI-MI-short [] synonym: "N4-(ADP-ribosyl)-L-asparagine" EXACT PSI-MI-alternate [] synonym: "N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine" EXACT PSI-MI-alternate [] synonym: "N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0533 name: glycosylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00693." [PMID:14755292] is_obsolete: true [Term] id: MI:0534 name: glycosyl-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00131." [PMID:14755292, RESID:AA0122] synonym: "S-glycosyl-L-cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0535 name: glycosyl-serine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00163." [PMID:14755292, RESID:AA0154] synonym: "O-glycosyl-L-serine" EXACT PSI-MI-alternate [] synonym: "O3-glycosyl-L-serine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0536 name: glycosyl-threonine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00164." [PMID:14755292, RESID:AA0155] synonym: "O-glycosyl-L-threonine" EXACT PSI-MI-alternate [] synonym: "O3-glycosyl-L-threonine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0537 name: omega-n-glycosyl-arginine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00332." [PMID:14755292, RESID:AA0327] synonym: "glycosylarginine" EXACT PSI-MI-short [] synonym: "omega-N-glycosyl-L-arginine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0538 name: n4-glycosyl-asparagine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00160." [PMID:14755292, RESID:AA0151] synonym: "glycosylasparagine" EXACT PSI-MI-short [] synonym: "N4-glycosyl-L-asparagine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0539 name: gpi anchor residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00818." [PMID:14755292] is_obsolete: true [Term] id: MI:0540 name: gpi-anchor amidated alanine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00172." [PMID:14755292, RESID:AA0163] synonym: "gpi-alanine" EXACT PSI-MI-short [] synonym: "N-alanyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0541 name: gpi-anchor amidated asparagine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00167." [PMID:14755292, RESID:AA0158] synonym: "gpi-asparagine" EXACT PSI-MI-short [] synonym: "N-asparaginyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0542 name: gpi-anchor amidated aspartate namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00168." [PMID:14755292, RESID:AA0159] synonym: "gpi-aspartate" EXACT PSI-MI-short [] synonym: "N-aspartyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0543 name: gpi-anchor amidated cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00169." [PMID:14755292, RESID:AA0160] synonym: "gpi-cysteine" EXACT PSI-MI-short [] synonym: "N-cysteinyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0544 name: gpi-anchor amidated glycine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00170." [PMID:14755292, RESID:AA0161] synonym: "gpi-glycine" EXACT PSI-MI-short [] synonym: "N-glycyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0545 name: gpi-anchor amidated serine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00171." [PMID:14755292, RESID:AA0162] synonym: "gpi-serine" EXACT PSI-MI-short [] synonym: "N-seryl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0546 name: gpi-anchor amidated threonine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00173." [PMID:14755292, RESID:AA0164] synonym: "gpi-threonine" EXACT PSI-MI-short [] synonym: "N-threonyl-glycosylphosphatidylinositolethanolamine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0547 name: s-prenyl-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:01110." [PMID:14755292] synonym: "prenylcysteine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0548 name: methylated-lysine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00663." [PMID:14755292, RESID:AA0074, RESID:AA0075, RESID:AA0076] synonym: "methylatedlysine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0549 name: alkylated cysteine namespace: PSI-MI def: "Artificial residue modification enabling studies of cysteine binding status.\nOBSOLETE remap to MOD:00660." [PMID:15325307] is_obsolete: true [Term] id: MI:0550 name: gamma-carboxyglutamic acid namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00041." [PMID:14755292, RESID:AA0032] synonym: "(S)-3-amino-1,1,3-propanetricarboxylic acid" EXACT PSI-MI-alternate [] synonym: "1-carboxyglutamic acid [misnomer]" EXACT PSI-MI-alternate [] synonym: "4-carboxyglutamic acid" EXACT PSI-MI-alternate [] synonym: "carboxyglutamic acid" EXACT PSI-MI-short [] synonym: "L-gamma-carboxyglutamic acid" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0551 name: nitro-tyrosine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00461." [PMID:15657065, PMID:9636206] synonym: "nitrated tyrosine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0552 name: s-nitrosyl-cysteine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00235." [PMID:14755292, RESID:AA0230] synonym: "(R)-2-amino-3-nitrososulfanyl-propanoic acid" EXACT PSI-MI-alternate [] synonym: "L-cysteine nitrite ester" EXACT PSI-MI-alternate [] synonym: "nitrosylcysteine" EXACT PSI-MI-short [] synonym: "S-nitrosocysteine" EXACT PSI-MI-alternate [] synonym: "S-nitrosyl-L-cysteine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0553 name: o4'-sulfo-tyrosine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00181." [PMID:14755292, RESID:AA0172] synonym: "(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid" EXACT PSI-MI-alternate [] synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate" EXACT PSI-MI-alternate [] synonym: "O4'-sulfo-L-tyrosine" EXACT PSI-MI-alternate [] synonym: "O4-sulfotyrosine" EXACT PSI-MI-alternate [] synonym: "sulfotyrosine" EXACT PSI-MI-short [] synonym: "tyrosine sulfate" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0554 name: sumoylated lysine namespace: PSI-MI def: "Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein.\nOBSOLETE remap to MOD:01149." [PMID:12612601, RESID:AA0125] synonym: "(S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid" EXACT PSI-MI-alternate [] synonym: "N6-glycyl-L-lysine" EXACT PSI-MI-alternate [] synonym: "N6-glycyllysine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0555 name: phospho-histidine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00890." [PMID:14755292, RESID:AA0035, RESID:AA0036] synonym: "phosphoshistidine" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0556 name: transglutamination reaction namespace: PSI-MI def: "Gln-Lys cross-link catalyzed by a transglutaminase." [PMID:14755292, RESID:AA0124] subset: PSI-MI_slim synonym: "transglutamination" EXACT PSI-MI-short [] is_a: MI:0195 ! covalent binding [Term] id: MI:0557 name: adp ribosylation reaction namespace: PSI-MI def: "Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues." [GO:0006471, PMID:14755292, RESID:AA0168, RESID:AA0169, RESID:AA0231, RESID:AA0237, RESID:AA0295] subset: PSI-MI_slim synonym: "adp ribosylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0558 name: deglycosylation reaction namespace: PSI-MI def: "Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins." [GO:0006517, PMID:15670854] subset: PSI-MI_slim synonym: "deglycosylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0559 name: glycosylation reaction namespace: PSI-MI def: "The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate." [GO:0043413, PMID:14755292, RESID:AA0122, RESID:AA0151, RESID:AA0154, RESID:AA0155, RESID:AA0327] subset: PSI-MI_slim synonym: "glycosylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0560 name: myristoylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00438." [PMID:14755292] synonym: "myristoylated aa" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0561 name: palmitoylated residue namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00440." [PMID:14755292] synonym: "palmitoylated aa" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0562 name: methylated alanine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00665." [PMID:14755292, RESID:AA0061, RESID:AA0062] is_obsolete: true [Term] id: MI:0563 name: methylated arginine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00658." [PMID:14755292, RESID:AA0068, RESID:AA0069] is_obsolete: true [Term] id: MI:0564 name: omega-n-methyl-arginine namespace: PSI-MI def: "Residue modification.\nOBSOLETE remap to MOD:00078." [PMID:14755292, RESID:AA0069] synonym: "(S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid" EXACT PSI-MI-alternate [] synonym: "methylarginine" EXACT PSI-MI-short [] synonym: "NG-methylarginine;" EXACT PSI-MI-alternate [] synonym: "omega-N-methyl-L-arginine" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0565 name: neddylated lysine namespace: PSI-MI def: "Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family.\nOBSOLETE remap to MOD:01150." [PMID:111] is_obsolete: true [Term] id: MI:0566 name: sumoylation reaction namespace: PSI-MI def: "Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." [GO:0016925, PMID:15985640] subset: PSI-MI_slim synonym: "sumoylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0567 name: neddylation reaction namespace: PSI-MI def: "Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." [GO:0045116, PMID:16127432] subset: PSI-MI_slim synonym: "neddylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0568 name: desumoylation reaction namespace: PSI-MI def: "Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins." [GO:0016926, PMID:15985640] subset: PSI-MI_slim synonym: "desumoylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0569 name: deneddylation reaction namespace: PSI-MI def: "Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome." [GO:0000338, PMID:16127432] subset: PSI-MI_slim synonym: "deneddylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0570 name: protein cleavage namespace: PSI-MI def: "Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation." [PMID:14744292] subset: PSI-MI_slim is_a: MI:0194 ! cleavage reaction [Term] id: MI:0571 name: mrna cleavage namespace: PSI-MI def: "Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner." [GO:0006379, PMID:14681407] subset: PSI-MI_slim is_a: MI:0902 ! rna cleavage [Term] id: MI:0572 name: dna cleavage namespace: PSI-MI def: "Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0910 ! nucleic acid cleavage [Term] id: MI:0573 name: mutation disrupting interaction namespace: PSI-MI def: "Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction).." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation disrupting" EXACT PSI-MI-short [] is_a: MI:0119 ! mutation decreasing interaction [Term] id: MI:0574 name: digital object identifier namespace: PSI-MI def: "Identifier of a publication prior to pubmed indexing." [PMID:14755292] subset: PSI-MI_slim synonym: "doi" EXACT PSI-MI-short [] xref: id-validation-regexp:\"\\d+.\\d+/[a-zA-Z0-9\\.\\\:\]+\" xref: search-url: "http://dx.doi.org/${ac}" is_a: MI:0445 ! literature database [Term] id: MI:0575 name: alliance for cellular signaling namespace: PSI-MI def: "Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all.\nhttp://www.signaling-gateway.org" [PMID:14755292] subset: PSI-MI_slim synonym: "AfCS" EXACT PSI-MI-alternate [] synonym: "afcs" EXACT PSI-MI-short [] xref: id-validation-regexp:\"[0-9\]+\" xref: search-url: "http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi?id=${ac}" is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0576 name: structural proximity namespace: PSI-MI def: "Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact." [PMID:15353450] subset: PSI-MI_slim is_a: MI:0577 ! feature prediction from structure [Term] id: MI:0577 name: feature prediction from structure namespace: PSI-MI def: "Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "feature struct pred" EXACT PSI-MI-short [] is_a: MI:0660 ! feature prediction [Term] id: MI:0578 name: maltose binding protein tag namespace: PSI-MI def: "The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin." [PMID:14755292] subset: PSI-MI_slim synonym: "maltose binding protein tag" EXACT PSI-MI-alternate [] synonym: "mbp tag" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0579 name: electron donor namespace: PSI-MI def: "Any molecule that is able to transfer an electron to another chemical species." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0918 ! donor [Term] id: MI:0580 name: electron acceptor namespace: PSI-MI def: "Molecule to which an electron may be transferred from an electron donor." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0919 ! acceptor [Term] id: MI:0581 name: suppressor gene namespace: PSI-MI def: "Gene whose mutation suppress the phenotype associated to a suppressed mutation." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0582 name: suppressed gene namespace: PSI-MI def: "Gene whose mutation phenotype is suppressed by a given suppressor mutation." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0583 name: fluorescence donor namespace: PSI-MI def: "Fluorophore which emits electromagnetic radiation of given wavelength." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role [Term] id: MI:0584 name: fluorescence acceptor namespace: PSI-MI def: "Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, the re-emission of its own characteristic fluorescence." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescence accept" EXACT PSI-MI-short [] is_a: MI:0495 ! experimental role [Term] id: MI:0585 name: intenz namespace: PSI-MI def: "IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at.\nhttp://www.ebi.ac.uk/intenz" [PMID:14681451] subset: PSI-MI_slim xref: id-validation-regexp:\"[0-6\]\{1}\\.(\\d+|-)\\.(\\d+|-)\\.(\\d+|-)\" xref: search-url: "http://www.ebi.ac.uk/intenz/query?cmd=Search&q=${ac}&t=exact&fields=ec" is_a: MI:0461 ! interaction database [Term] id: MI:0586 name: inhibitor namespace: PSI-MI def: "Molecule inhibiting an interaction by interacting with one or more of its participants." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0500 ! biological role [Term] id: MI:0587 name: inhibited namespace: PSI-MI def: "Molecule being identified as target of an inhibitor.\nOBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role." [PMID:14755292] subset: PSI-MI_slim is_obsolete: true [Term] id: MI:0588 name: three hybrid namespace: PSI-MI def: "Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey." [PMID:14755292] subset: PSI-MI_slim synonym: "3 hybrid" EXACT PSI-MI-short [] synonym: "3-hybrid" EXACT PSI-MI-alternate [] synonym: "tri hybrid" EXACT PSI-MI-alternate [] synonym: "tri-hybrid assay" EXACT PSI-MI-alternate [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0589 name: in vitro translated protein namespace: PSI-MI def: "Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery." [PMID:14755292] subset: PSI-MI_slim synonym: "in vitro translated" EXACT PSI-MI-short [] is_a: MI:0342 ! sample process [Term] id: MI:0590 name: attribute name namespace: PSI-MI def: "Collection of topics describing the free text stored as an attribute value." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "CvTopic" EXACT PSI-MI-alternate [] relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0591 name: experiment description namespace: PSI-MI def: "The experimental condition text description, should contain information about the organisms hosting the interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "experiment descripti" EXACT PSI-MI-short [] is_a: MI:0665 ! experiment attibute name [Term] id: MI:0592 name: ipfam namespace: PSI-MI def: "Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at.\nhttp://www.sanger.ac.uk/Software/Pfam/iPfam/" [PMID:15353450] subset: PSI-MI_slim is_a: MI:0447 ! feature database [Term] id: MI:0593 name: translocation namespace: PSI-MI def: "Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'." [PMID:14681407] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0594 name: translocation start namespace: PSI-MI def: "Xref pointing to a GO compartment term describing the start location of a migrating molecule." [PMID:14681407] subset: PSI-MI_slim is_a: MI:0593 ! translocation [Term] id: MI:0595 name: translocation end namespace: PSI-MI def: "Xref pointing to a GO compartment term describing the end location of a migrating molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0593 ! translocation [Term] id: MI:0596 name: experimental form description namespace: PSI-MI def: "Free text description of all the tags and artificial process undergone by a molecule during an experiment." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental form de" EXACT PSI-MI-short [] is_a: MI:0666 ! participant attribute name [Term] id: MI:0597 name: feature description namespace: PSI-MI def: "The feature text description may include information about the feature detection method." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0668 ! feature attribute name [Term] id: MI:0598 name: feature constraint namespace: PSI-MI def: "The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0668 ! feature attribute name [Term] id: MI:0599 name: figure legend namespace: PSI-MI def: "Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attibute name [Term] id: MI:0600 name: conditional synthetic lethal nutrition-sensitivity namespace: PSI-MI def: "Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell.\nOBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description." [PMID:15608217] subset: PSI-MI_slim synonym: "nutrition synt letal" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0601 name: sequence ontology namespace: PSI-MI def: "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data." [PMID:15892872] subset: PSI-MI_slim synonym: "so" EXACT PSI-MI-short [] xref: id-validation-regexp:\"SO\:[0-9\]\{7}\" is_a: MI:0447 ! feature database is_a: MI:0473 ! participant database [Term] id: MI:0602 name: chemical footprinting namespace: PSI-MI def: "Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo." [PMID:8238889] subset: PSI-MI_slim synonym: "chemical footprint" EXACT PSI-MI-short [] is_a: MI:0417 ! footprinting [Term] id: MI:0603 name: dimethylsulphate footprinting namespace: PSI-MI def: "Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction." [PMID:8238889] subset: PSI-MI_slim synonym: "dms footprinting" EXACT PSI-MI-short [] is_a: MI:0602 ! chemical footprinting [Term] id: MI:0604 name: potassium permanganate footprinting namespace: PSI-MI def: "Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control." [PMID:8238889] subset: PSI-MI_slim synonym: "k-mn-04 footprinting" EXACT PSI-MI-short [] is_a: MI:0602 ! chemical footprinting [Term] id: MI:0605 name: enzymatic footprinting namespace: PSI-MI def: "Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo." [PMID:8238889] subset: PSI-MI_slim synonym: "enzymatic footprint" EXACT PSI-MI-short [] is_a: MI:0417 ! footprinting [Term] id: MI:0606 name: DNase I footprinting namespace: PSI-MI def: "Deoxyribonuclease I (DNase I) do not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA." [PMID:8238889] subset: PSI-MI_slim synonym: "dnase 1 footprinting" EXACT PSI-MI-short [] is_a: MI:0605 ! enzymatic footprinting [Term] id: MI:0607 name: small nuclear rna namespace: PSI-MI def: "These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome." [PMID:14755292] subset: PSI-MI_slim synonym: "snRNA" EXACT PSI-MI-alternate [] synonym: "snrna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0608 name: ribosomal rna namespace: PSI-MI def: "RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes." [PMID:14755292] subset: PSI-MI_slim synonym: "rRNA" EXACT PSI-MI-alternate [] synonym: "rrna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0609 name: small nucleolar rna namespace: PSI-MI def: "The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA." [PMID:14755292] subset: PSI-MI_slim synonym: "snoRNA" EXACT PSI-MI-alternate [] synonym: "snorna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0610 name: small interfering rna namespace: PSI-MI def: "Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression." [PMID:10542148] subset: PSI-MI_slim synonym: "dicer RNA" EXACT PSI-MI-alternate [] synonym: "micro RNA" EXACT PSI-MI-alternate [] synonym: "siRNA" EXACT PSI-MI-alternate [] synonym: "sirna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0611 name: signal recognition particle rna namespace: PSI-MI def: "Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane." [PMID:14755292] subset: PSI-MI_slim synonym: "srpRNA" EXACT PSI-MI-alternate [] synonym: "srprna" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0612 name: comment namespace: PSI-MI def: "Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attibute name is_a: MI:0666 ! participant attribute name is_a: MI:0667 ! controlled vocabulary attribute name is_a: MI:0668 ! feature attribute name is_a: MI:0669 ! organism attribute name [Term] id: MI:0613 name: function namespace: PSI-MI def: "Biological function of a participant or of an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0666 ! participant attribute name [Term] id: MI:0614 name: url namespace: PSI-MI def: "URL/Web address describing an experiment, an interaction, a Cv term or an organism." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attibute name is_a: MI:0667 ! controlled vocabulary attribute name is_a: MI:0669 ! organism attribute name [Term] id: MI:0615 name: search-url namespace: PSI-MI def: "Search engine URL associated to Cv Database terms." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0667 ! controlled vocabulary attribute name [Term] id: MI:0616 name: example namespace: PSI-MI def: "Example generally associated to Cv terms. Test." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0667 ! controlled vocabulary attribute name is_a: MI:1041 ! synonym [Term] id: MI:0617 name: disease namespace: PSI-MI def: "The interaction has a known or demonstrated disease association." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0618 name: caution namespace: PSI-MI def: "Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attibute name is_a: MI:0666 ! participant attribute name is_a: MI:0667 ! controlled vocabulary attribute name is_a: MI:0668 ! feature attribute name is_a: MI:0669 ! organism attribute name [Term] id: MI:0619 name: pathway namespace: PSI-MI def: "Refers to the metabolic or signalling pathway involving an interaction or a complex." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0620 name: search-url-ascii namespace: PSI-MI def: "Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0667 ! controlled vocabulary attribute name [Term] id: MI:0621 name: author-confidence namespace: PSI-MI def: "Confidence classification assigned by the author of the publication to a specific interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0622 name: confidence-mapping namespace: PSI-MI def: "Description of confidence assessment method generally associated to the experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attibute name [Term] id: MI:0623 name: inhibition namespace: PSI-MI def: "The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0624 name: stimulant namespace: PSI-MI def: "Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0625 name: agonist namespace: PSI-MI def: "Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0626 name: antagonist namespace: PSI-MI def: "Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0627 name: experiment modification namespace: PSI-MI def: "Modifications of the standard experimental method described in the CV." [PMID:14755292] subset: PSI-MI_slim synonym: "exp-modification" EXACT PSI-MI-short [] is_a: MI:0665 ! experiment attibute name [Term] id: MI:0628 name: validation regular expression namespace: PSI-MI def: "Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database." [PMID:14755292] subset: PSI-MI_slim synonym: "id-validation-regexp" EXACT PSI-MI-short [] is_a: MI:0667 ! controlled vocabulary attribute name [Term] id: MI:0629 name: complex-properties namespace: PSI-MI def: "Information on the complex being annotated. Attribute generally associated to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0665 ! experiment attibute name [Term] id: MI:0630 name: 3d-structure namespace: PSI-MI def: "Comments on the 3D structure. This attribute is generally associated to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0631 name: 3d-r-factors namespace: PSI-MI def: "Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0632 name: 3d-resolution namespace: PSI-MI def: "Resolution of the 3D structure. This attribute is generally associated to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name [Term] id: MI:0633 name: data-processing namespace: PSI-MI def: "Information about how the data was processed. This attribute is used mainly for large scale experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attibute name [Term] id: MI:0634 name: contact-email namespace: PSI-MI def: "E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0635 name: contact-comment namespace: PSI-MI def: "Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0636 name: author-list namespace: PSI-MI def: "List of authors associated to a publication. This attribute is generally associated to an experiment." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0637 name: isoform-comment namespace: PSI-MI def: "Participant isoform's comment. This attribute can be attached to interactions or participants." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0664 ! interaction attribute name is_a: MI:0666 ! participant attribute name [Term] id: MI:0638 name: prerequisite-ptm namespace: PSI-MI def: "Post translational modification required for an interaction to occur." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0925 ! observed ptm [Term] id: MI:0639 name: resulting-ptm namespace: PSI-MI def: "Post translational modification occurs subsequently to an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0925 ! observed ptm [Term] id: MI:0640 name: parameter type namespace: PSI-MI def: "Parameter for enzymatic or binding kinetic studies." [PMID:14755292] subset: Drugable subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0641 name: ic50 namespace: PSI-MI def: "Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar." [PMID:14755292] subset: PSI-MI_slim synonym: "IC50" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0642 name: ec50 namespace: PSI-MI def: "Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar." [PMID:14755292] subset: PSI-MI_slim synonym: "EC50" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0643 name: ki namespace: PSI-MI def: "Equilibrium constant for dissociation of an inhibitor. Unit Molar." [PMID:14755292] subset: PSI-MI_slim synonym: "Ki" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0644 name: km namespace: PSI-MI def: "Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar." [PMID:14755292] subset: PSI-MI_slim synonym: "Km" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0645 name: kcat namespace: PSI-MI def: "The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1." [PMID:14755292] subset: PSI-MI_slim synonym: "turnover number" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0646 name: Kd namespace: PSI-MI def: "The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1)." [PMID:14755292] subset: PSI-MI_slim synonym: "Kd" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0647 name: parameter unit namespace: PSI-MI def: "Controlled vocabulary for kinetic constant units." [PMID:14755292] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0648 name: molar namespace: PSI-MI def: "Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles)." [PMID:14755292] subset: PSI-MI_slim synonym: "M" EXACT PSI-MI-alternate [] is_a: MI:0647 ! parameter unit [Term] id: MI:0649 name: second namespace: PSI-MI def: "The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant." [PMID:14755292] subset: PSI-MI_slim synonym: "s" EXACT PSI-MI-alternate [] synonym: "sec" EXACT PSI-MI-alternate [] is_a: MI:0647 ! parameter unit [Term] id: MI:0650 name: millimolar namespace: PSI-MI def: "10E-3 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "mM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0651 name: micromolar namespace: PSI-MI def: "10E-6 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "uM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0652 name: nanomolar namespace: PSI-MI def: "10E-9 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "nM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0653 name: picomolar namespace: PSI-MI def: "10E-12 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "pM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0654 name: fentomolar namespace: PSI-MI def: "10E-15 moles per liter of solution.\nOBSOLETE: term redundant with the schema exponent attribute of the parameter." [PMID:14755292] subset: PSI-MI_slim synonym: "fM" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0655 name: lambda repressor two hybrid namespace: PSI-MI def: "A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization." [PMID:15792953] subset: PSI-MI_slim synonym: "BacterioMatch" EXACT PSI-MI-alternate [] synonym: "lambda two hybrid" EXACT PSI-MI-short [] is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0656 name: identified peptide namespace: PSI-MI def: "Peptide whose sequence is experimentally identified and can lead to a full protein identification." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0657 name: systematic evolution of ligands by exponential enrichment namespace: PSI-MI def: "RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing." [PMID:11539574] subset: PSI-MI_slim synonym: "in vitro evolution of nucleic acids" EXACT PSI-MI-alternate [] synonym: "selex" EXACT PSI-MI-short [] is_a: MI:0400 ! affinity technology [Term] id: MI:0658 name: multidimensional protein identification technology namespace: PSI-MI def: "MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified." [PMID:11231557] subset: PSI-MI_slim synonym: "mudpit" EXACT PSI-MI-short [] is_a: MI:0093 ! protein sequence identification is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0815 ! confirmation by molecular weight [Term] id: MI:0659 name: experimental feature detection namespace: PSI-MI def: "Experimental method by which a feature is detected or identified." [PMID:14755292] subset: PSI-MI_slim synonym: "exp feature detect" EXACT PSI-MI-short [] is_a: MI:0003 ! feature detection method [Term] id: MI:0660 name: feature prediction namespace: PSI-MI def: "Feature detection based on computational analysis." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0003 ! feature detection method [Term] id: MI:0661 name: experimental participant identification namespace: PSI-MI def: "experimental participant identification." [PMID:14755292] subset: PSI-MI_slim synonym: "experimental particp" EXACT PSI-MI-short [] is_a: MI:0002 ! participant identification method [Term] id: MI:0662 name: imex-primary namespace: PSI-MI def: "IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner.\nhttp://imex.sourceforge.net/" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0663 name: confocal microscopy namespace: PSI-MI def: "A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0428 ! imaging technique [Term] id: MI:0664 name: interaction attribute name namespace: PSI-MI def: "Attribute name of annotation associated to an interaction element." [PMID:14755292] subset: PSI-MI_slim synonym: "interaction att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0665 name: experiment attibute name namespace: PSI-MI def: "Attribute name of annotation associated to an experiment element." [PMID:14755292] subset: PSI-MI_slim synonym: "experiment att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0666 name: participant attribute name namespace: PSI-MI def: "Attribute name of annotation associated to a participant element." [PMID:14755292] subset: PSI-MI_slim synonym: "participant att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0667 name: controlled vocabulary attribute name namespace: PSI-MI def: "Attribute name of annotation associated to a CV term." [PMID:14755292] subset: PSI-MI_slim synonym: "cv att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0668 name: feature attribute name namespace: PSI-MI def: "Attribute name of annotation associated to a feature element." [PMID:14755292] subset: PSI-MI_slim synonym: "feature att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0669 name: organism attribute name namespace: PSI-MI def: "Attribute name of annotation associated to an organism element." [PMID:14755292] subset: PSI-MI_slim synonym: "organism att name" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:0670 name: imex namespace: PSI-MI def: "International Molecular Interaction Exchange." [PMID:14755292] subset: PSI-MI_slim synonym: "IMEx" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database [Term] id: MI:0671 name: antibodies namespace: PSI-MI def: "This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attibute name [Term] id: MI:0672 name: library-used namespace: PSI-MI def: "This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attibute name [Term] id: MI:0673 name: complex-synonym namespace: PSI-MI def: "Alternative names to describe a complex." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1041 ! synonym [Term] id: MI:0674 name: peptide parent sequence reference namespace: PSI-MI def: "Describe a cross reference pointing to a peptide parent sequence." [PMID:14755292] subset: PSI-MI_slim synonym: "peptide-parent" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0675 name: international protein index namespace: PSI-MI def: "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources." [PMID:15221759] subset: PSI-MI_slim synonym: "ipi" EXACT PSI-MI-short [] xref: id-validation-regexp:\"IPI[0-9\]+.[0-9\]+|IPI[0-9\]+\" is_a: MI:1096 ! protein sequence databases [Term] id: MI:0676 name: tandem affinity purification namespace: PSI-MI def: "Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification." [PMID:11403571] subset: PSI-MI_slim synonym: "TAP" EXACT PSI-MI-alternate [] synonym: "tap" EXACT PSI-MI-short [] is_a: MI:0004 ! affinity chromatography technology [Term] id: MI:0677 name: tandem tag namespace: PSI-MI def: "A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag [Term] id: MI:0678 name: antibody array namespace: PSI-MI def: "A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others)." [PMID:12454649] subset: PSI-MI_slim synonym: "antigen capture assay" EXACT PSI-MI-alternate [] synonym: "sandwich immunoassay" EXACT PSI-MI-alternate [] is_a: MI:0089 ! protein array [Term] id: MI:0679 name: poly adenine namespace: PSI-MI def: "A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "poly A" EXACT PSI-MI-alternate [] synonym: "poly a" EXACT PSI-MI-short [] is_a: MI:0320 ! ribonucleic acid [Term] id: MI:0680 name: single stranded deoxyribonucleic acid namespace: PSI-MI def: "DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form." [PMID:14755292] subset: PSI-MI_slim synonym: "ss DNA" EXACT PSI-MI-alternate [] synonym: "ss dna" EXACT PSI-MI-short [] is_a: MI:0319 ! deoxyribonucleic acid [Term] id: MI:0681 name: double stranded deoxyribonucleic acid namespace: PSI-MI def: "DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.\n" [PMID:14755292] subset: PSI-MI_slim synonym: "ds DNA" EXACT PSI-MI-alternate [] synonym: "ds dna" EXACT PSI-MI-short [] is_a: MI:0319 ! deoxyribonucleic acid [Term] id: MI:0682 name: cofactor namespace: PSI-MI def: "A cofactor is a small molecule required for the catalysis of an enzyme." [PMID:14755292] subset: PSI-MI_slim synonym: "coenzyme" EXACT PSI-MI-alternate [] is_a: MI:0500 ! biological role [Term] id: MI:0683 name: sequence database namespace: PSI-MI def: "Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0473 ! participant database [Term] id: MI:0684 name: ancillary namespace: PSI-MI def: "Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role is_a: MI:0500 ! biological role [Term] id: MI:0685 name: source reference namespace: PSI-MI def: "Publication or document describing the originating resource where an interaction, or other curated information, was first described." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0686 name: unspecified method namespace: PSI-MI def: "Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation." [PMID:14755292] subset: Drugable subset: PSI-MI_slim is_a: MI:0001 ! interaction detection method [Term] id: MI:0687 name: fluorescent protein tag namespace: PSI-MI def: "Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescent prot tag" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0688 name: dna binding domain tag namespace: PSI-MI def: "Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag." [PMID:14755292] subset: PSI-MI_slim synonym: "dna binding domain" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0689 name: activation domain tag namespace: PSI-MI def: "Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag." [PMID:14755292] subset: PSI-MI_slim synonym: "activation domain" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0690 name: gal4 activation domain namespace: PSI-MI def: "Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation." [PMID:14755292] subset: PSI-MI_slim synonym: "gal4 ad" EXACT PSI-MI-short [] is_a: MI:0689 ! activation domain tag [Term] id: MI:0691 name: vp16 activation domain namespace: PSI-MI def: "Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor." [PMID:14755292] subset: PSI-MI_slim synonym: "vp16 ad" EXACT PSI-MI-short [] is_a: MI:0689 ! activation domain tag [Term] id: MI:0692 name: b42 activation domain namespace: PSI-MI def: "B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection." [PMID:14613974] subset: PSI-MI_slim synonym: "b42 ad" EXACT PSI-MI-short [] is_a: MI:0689 ! activation domain tag [Term] id: MI:0693 name: gal4 dna binding domain namespace: PSI-MI def: "Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.\n" [PMID:14755292] subset: PSI-MI_slim synonym: "gal4 dna bd" EXACT PSI-MI-short [] is_a: MI:0688 ! dna binding domain tag [Term] id: MI:0694 name: lexa dna binding domain namespace: PSI-MI def: "Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "lexa dna bd" EXACT PSI-MI-short [] is_a: MI:0688 ! dna binding domain tag [Term] id: MI:0695 name: sandwich immunoassay namespace: PSI-MI def: "Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin." [PMID:12454649] subset: PSI-MI_slim is_a: MI:0678 ! antibody array [Term] id: MI:0696 name: polymerase assay namespace: PSI-MI def: "Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain." [PMID:14755292] subset: PSI-MI_slim synonym: "nucleotidyltransferase assay" EXACT PSI-MI-alternate [] is_a: MI:0415 ! enzymatic study [Term] id: MI:0697 name: dna directed dna polymerase assay namespace: PSI-MI def: "Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer." [PMID:14755292] subset: PSI-MI_slim synonym: "dna dna pol assay" EXACT PSI-MI-short [] is_a: MI:0696 ! polymerase assay [Term] id: MI:0698 name: dna directed rna polymerase assay namespace: PSI-MI def: "Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [PMID:14755292] subset: PSI-MI_slim synonym: "dna rna pol assay" EXACT PSI-MI-short [] is_a: MI:0696 ! polymerase assay [Term] id: MI:0699 name: rna directed dna polymerase assay namespace: PSI-MI def: "Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time." [PMID:14755292] subset: PSI-MI_slim synonym: "rna dna pol assay" EXACT PSI-MI-short [] is_a: MI:0696 ! polymerase assay [Term] id: MI:0700 name: rna directed rna polymerase assay namespace: PSI-MI def: "Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template." [PMID:14755292] subset: PSI-MI_slim synonym: "rna rna pol assay" EXACT PSI-MI-short [] is_a: MI:0696 ! polymerase assay [Term] id: MI:0701 name: dna strand elongation namespace: PSI-MI def: "The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand." [GO:0006271, PMID:14755292] subset: PSI-MI_slim synonym: "dna elongation" EXACT PSI-MI-short [] synonym: "DNA replication elongation " EXACT PSI-MI-alternate [] is_a: MI:0986 ! nucleic acid strand elongation reaction [Term] id: MI:0702 name: panther namespace: PSI-MI def: "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.\nwww.pantherdb.org/" [PMID:14755292] subset: PSI-MI_slim synonym: "PANTHER" EXACT PSI-MI-alternate [] is_a: MI:0449 ! interpro [Term] id: MI:0703 name: gene3d namespace: PSI-MI def: "The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species.\nhttp://cathwww.biochem.ucl.ac.uk:8080/Gene3D/" [PMID:14755292] subset: PSI-MI_slim synonym: "Gene3D" EXACT PSI-MI-alternate [] is_a: MI:0449 ! interpro [Term] id: MI:0704 name: nucleic acid delivery namespace: PSI-MI def: "Method by which nucleic acids are delivered or engineered into a cell." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl delivery" EXACT PSI-MI-short [] is_a: MI:0307 ! delivery method [Term] id: MI:0705 name: anti tag western blot namespace: PSI-MI def: "Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal." [PMID:14755292] subset: PSI-MI_slim synonym: "anti tag western" EXACT PSI-MI-short [] is_a: MI:0113 ! western blot is_a: MI:0866 ! tag visualisation [Term] id: MI:0706 name: nucleic acid transformation namespace: PSI-MI def: "Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA)." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl transformation" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0707 name: anti tag immunostaining namespace: PSI-MI def: "Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal." [PMID:14755292] subset: PSI-MI_slim synonym: "anti tag immunost" EXACT PSI-MI-short [] is_a: MI:0422 ! immunostaining [Term] id: MI:0708 name: monoclonal antibody immunostaining namespace: PSI-MI def: "A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample." [PMID:14755292] subset: PSI-MI_slim synonym: "monoclonal immunost" EXACT PSI-MI-short [] is_a: MI:0422 ! immunostaining [Term] id: MI:0709 name: polyclonal antibody immunostaining namespace: PSI-MI def: "Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample." [PMID:14755292] subset: PSI-MI_slim synonym: "polyclonal immunost" EXACT PSI-MI-short [] is_a: MI:0422 ! immunostaining [Term] id: MI:0710 name: nucleic acid transformation by treatment with divalent cation namespace: PSI-MI def: "Stable introduction and expression of nucleic acid carried out by treatment with divalent cation." [PMID:14755292] subset: PSI-MI_slim synonym: "n transformat cation" EXACT PSI-MI-short [] is_a: MI:0706 ! nucleic acid transformation [Term] id: MI:0711 name: nucleic acid electroporation namespace: PSI-MI def: "Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl electroporation" EXACT PSI-MI-short [] is_a: MI:0308 ! electroporation is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0712 name: nucleic acid microinjection namespace: PSI-MI def: "Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl microinjection" EXACT PSI-MI-short [] is_a: MI:0311 ! microinjection is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0713 name: nucleic acid passive uptake namespace: PSI-MI def: "Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl passive uptake" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery is_a: MI:0716 ! passive uptake [Term] id: MI:0714 name: nucleic acid transduction namespace: PSI-MI def: "Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl transduction" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0715 name: nucleic acid conjugation namespace: PSI-MI def: "Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient" [PMID:14755292] subset: PSI-MI_slim synonym: "nucl conjugation" EXACT PSI-MI-short [] is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0716 name: passive uptake namespace: PSI-MI def: "Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0307 ! delivery method [Term] id: MI:0717 name: nucleic acid transfection with liposome namespace: PSI-MI def: "Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl lipotransfect" EXACT PSI-MI-short [] is_a: MI:0312 ! nucleic acid transfection [Term] id: MI:0718 name: nucleic acid transfection by treatment namespace: PSI-MI def: "Transient introduction and expression of nucleic acid carried out by treatment with chemicals." [PMID:14755292] subset: PSI-MI_slim synonym: "n transfection treat" EXACT PSI-MI-short [] is_a: MI:0312 ! nucleic acid transfection [Term] id: MI:0719 name: calcium phosphate nucleic acid transfection namespace: PSI-MI def: "Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate." [PMID:14755292] subset: PSI-MI_slim synonym: "ca po nuc transfect" EXACT PSI-MI-short [] is_a: MI:0718 ! nucleic acid transfection by treatment [Term] id: MI:0720 name: nucleic acid delivery by infection namespace: PSI-MI def: "Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria.." [PMID:14755292] subset: PSI-MI_slim synonym: "nucl infection" EXACT PSI-MI-short [] is_a: MI:0310 ! infection is_a: MI:0704 ! nucleic acid delivery [Term] id: MI:0721 name: protein delivery namespace: PSI-MI def: "Method by which proteins are delivered into a cell." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0307 ! delivery method [Term] id: MI:0722 name: protein electroporation namespace: PSI-MI def: "Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein." [PMID:14755292] subset: PSI-MI_slim synonym: "prot electroporation" EXACT PSI-MI-short [] is_a: MI:0308 ! electroporation is_a: MI:0721 ! protein delivery [Term] id: MI:0723 name: protein microinjection namespace: PSI-MI def: "Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins." [PMID:14755292] subset: PSI-MI_slim synonym: "prot microinjection" EXACT PSI-MI-short [] is_a: MI:0311 ! microinjection is_a: MI:0721 ! protein delivery [Term] id: MI:0724 name: protein delivery by cationic lipid treatment namespace: PSI-MI def: "Proteins are delivered into cells by treatment with cationic lipids." [PMID:14755292] subset: PSI-MI_slim synonym: "prot cationic lipid" EXACT PSI-MI-short [] is_a: MI:0721 ! protein delivery [Term] id: MI:0725 name: protein delivery by infection namespace: PSI-MI def: "Protein introduced into a cell via an external organism, usually a virus or bacteria." [PMID:14755292] subset: PSI-MI_slim synonym: "prot infection" EXACT PSI-MI-short [] is_a: MI:0310 ! infection is_a: MI:0721 ! protein delivery [Term] id: MI:0726 name: reverse two hybrid namespace: PSI-MI def: "Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site." [PMID:8816797] subset: PSI-MI_slim is_a: MI:0232 ! transcriptional complementation assay [Term] id: MI:0727 name: lexa b52 complementation namespace: PSI-MI def: "Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements." [PMID:14613974] subset: PSI-MI_slim synonym: "lexa b52 complement" EXACT PSI-MI-short [] synonym: "LexA B52 transcription complementation" EXACT PSI-MI-alternate [] is_a: MI:0018 ! two hybrid [Term] id: MI:0728 name: gal4 vp16 complementation namespace: PSI-MI def: "A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated." [PMID:1387709] subset: PSI-MI_slim synonym: "gal4 vp16 complement" EXACT PSI-MI-short [] synonym: "karyoplasmic interaction ion strategy" EXACT PSI-MI-alternate [] synonym: "KISS" EXACT PSI-MI-alternate [] synonym: "mammalian two hybrid" EXACT PSI-MI-alternate [] is_a: MI:0018 ! two hybrid [Term] id: MI:0729 name: luminescence based mammalian interactome mapping namespace: PSI-MI def: "This strategy uses Renilla luciferase enzyme (RL) fused to proteins of interest, which are then coexpressed with individual Flag-tagged partners in mammalian cells. Their interactions are determined by performing an RL enzymatic assay on anti-Flag immunoprecipitates." [PMID:15761153] subset: PSI-MI_slim synonym: "lumier" EXACT PSI-MI-short [] is_a: MI:0004 ! affinity chromatography technology [Term] id: MI:0730 name: pubchem namespace: PSI-MI def: "PubChem provides information on the biological activities of small molecules.\nhttp://pubchem.ncbi.nlm.nih.gov/" [PMID:16381840] subset: PSI-MI_slim synonym: "PubChem" EXACT PSI-MI-alternate [] is_a: MI:2054 ! bioactive entity reference [Term] id: MI:0731 name: 3d repertoire namespace: PSI-MI def: "The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository." [PMID:14755292] subset: PSI-MI_slim synonym: "3D Repertoire" EXACT PSI-MI-alternate [] is_a: MI:0489 ! source database [Term] id: MI:0732 name: red fluorescent protein tag namespace: PSI-MI def: "The red fluorescent protein derived from marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:14755292] subset: PSI-MI_slim synonym: "red fluorescent protein" EXACT PSI-MI-alternate [] synonym: "RFP" EXACT PSI-MI-alternate [] synonym: "rfp tag" EXACT PSI-MI-short [] is_a: MI:0687 ! fluorescent protein tag [Term] id: MI:0733 name: cyan fluorescent protein tag namespace: PSI-MI def: "The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:14755292] subset: PSI-MI_slim synonym: "CFP" EXACT PSI-MI-alternate [] synonym: "cfp tag" EXACT PSI-MI-short [] synonym: "cyan fluorescent protein" EXACT PSI-MI-alternate [] is_a: MI:0687 ! fluorescent protein tag [Term] id: MI:0734 name: enhanced green fluorescent protein tag namespace: PSI-MI def: "Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native." [PMID:14755292] subset: PSI-MI_slim synonym: "EGFP" EXACT PSI-MI-alternate [] synonym: "egfp tag" EXACT PSI-MI-short [] synonym: "enhanced green fluorescent protein" EXACT PSI-MI-alternate [] is_a: MI:0367 ! green fluorescent protein tag [Term] id: MI:0735 name: transactivating tag namespace: PSI-MI def: "Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells." [PMID:8290579] subset: PSI-MI_slim synonym: "Tat tag" EXACT PSI-MI-alternate [] synonym: "tat tag" EXACT PSI-MI-short [] is_a: MI:0740 ! cell penetrating peptide tag [Term] id: MI:0736 name: protein passive uptake namespace: PSI-MI def: "Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes." [PMID:14755292] subset: PSI-MI_slim synonym: "prot passive uptake" EXACT PSI-MI-short [] is_a: MI:0716 ! passive uptake is_a: MI:0721 ! protein delivery [Term] id: MI:0737 name: peptide sequence database namespace: PSI-MI def: "database storing sequences detected by peptide identification methods." [PMID:14755292] subset: PSI-MI_slim synonym: "pep seq db" EXACT PSI-MI-short [] is_a: MI:0683 ! sequence database [Term] id: MI:0738 name: pride namespace: PSI-MI def: "PRIDE is a public repository of protein and peptide identifications for the proteomics community.\nhttp://www.ebi.ac.uk/pride/" [PMID:16381953] subset: PSI-MI_slim xref: search-url: "http://www.ebi.ac.uk/pride/searchSummary.do?experimentCvAccession=PRIDE:0000156&queryTypeSelected=ExperimentCV&experimentCvValue=${ac}" is_a: MI:0737 ! peptide sequence database [Term] id: MI:0739 name: penetrating tag namespace: PSI-MI def: "Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK" [PMID:16574060] subset: PSI-MI_slim is_a: MI:0740 ! cell penetrating peptide tag [Term] id: MI:0740 name: cell penetrating peptide tag namespace: PSI-MI def: "The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus." [PMID:16574060] subset: PSI-MI_slim synonym: "cell penetrating pep" EXACT PSI-MI-short [] synonym: "cell-penetrating peptides" EXACT PSI-MI-alternate [] synonym: "CPPs" EXACT PSI-MI-alternate [] synonym: "membrane translocating sequences" EXACT PSI-MI-alternate [] synonym: "MTS" EXACT PSI-MI-alternate [] synonym: "protein transduction domains" EXACT PSI-MI-alternate [] synonym: "PTDs" EXACT PSI-MI-alternate [] synonym: "Trojan peptides" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0741 name: peptide atlas namespace: PSI-MI def: "PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms.\nhttp://www.peptideatlas.org/" [PMID:15642101, PMID:16381952] subset: PSI-MI_slim synonym: "PeptideAtlas" EXACT PSI-MI-alternate [] is_a: MI:0737 ! peptide sequence database [Term] id: MI:0742 name: gpm namespace: PSI-MI def: "Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results.\nhttp://www.thegpm.org" [PMID:15595733] subset: PSI-MI_slim synonym: "Global Proteome Machine" EXACT PSI-MI-alternate [] is_a: MI:0737 ! peptide sequence database [Term] id: MI:0787 name: genetic experimental form namespace: PSI-MI def: "Descriptor of an experimental form involved in a genetic interaction" [PMID:14755292] subset: PSI-MI_slim synonym: "genetic exp form" EXACT PSI-MI-short [] is_a: MI:0346 ! experimental preparation [Term] id: MI:0788 name: knock out namespace: PSI-MI def: "The gene has been completely removed e.g. by genetic engineering " [PMID:14755292] subset: PSI-MI_slim synonym: "knock-out" EXACT PSI-MI-short [] is_a: MI:0804 ! mutated gene [Term] id: MI:0789 name: knock down namespace: PSI-MI def: "The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference." [PMID:14755292] subset: PSI-MI_slim synonym: "knock-down" EXACT PSI-MI-short [] is_a: MI:0804 ! mutated gene [Term] id: MI:0790 name: hypermorph namespace: PSI-MI def: "The gene function has been partially improved compared to wild-type by altering its sequence." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0791 name: hypomorph namespace: PSI-MI def: "The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0792 name: antimorph namespace: PSI-MI def: "The gene function has been antagonized by a mutation in another copy of the gene." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0793 name: amorph namespace: PSI-MI def: "The gene function has been abolished by mutation, though the type of mutation is not known." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0794 name: synthetic genetic interaction defined by inequality namespace: PSI-MI def: "The phenotype resulting from genetic perturbation a and the phenotype resulting from genetic perturbation b have no effect on the WT background, but the combined genetic perturbation of A and B has a phenotypic effect. E. g., WT = a = b > ab." [PMID:15833125] subset: PSI-MI_slim synonym: "synthetic" EXACT PSI-MI-short [] synonym: "synthetic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0931 ! genetic interaction defined by inequality is_a: MI:0933 ! negative genetic interaction [Term] id: MI:0795 name: asynthetic genetic interaction defined by inequality namespace: PSI-MI def: "The phenotype resulting from genetic perturbation of A alone, B alone and AB combined have the same effect on the WT background. E. g., WT > a = b = ab." [PMID:15833125] subset: PSI-MI_slim synonym: "asynthetic" EXACT PSI-MI-short [] synonym: "asynthetic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0930 ! epistatic genetic interaction is_a: MI:0931 ! genetic interaction defined by inequality [Term] id: MI:0796 name: suppressive genetic interaction defined by inequality namespace: PSI-MI def: "The phenotype resulting from genetic perturbation of A has an effect on WT, but that effect is abolished by adding the suppressor b, which itself shows no single-mutant effect. E. g., WT = b = ab > a." [PMID:15833125] subset: PSI-MI_slim synonym: "suppression" EXACT PSI-MI-short [] synonym: "suppressive genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0930 ! epistatic genetic interaction is_a: MI:0931 ! genetic interaction defined by inequality [Term] id: MI:0797 name: epistatic genetic interaction defined by inequality namespace: PSI-MI def: "The phenotype resulting from genetic perturbation of A and B have different effects (in terms of direction or magnitude) on the wild-type background and the double mutant has the same phenotype as either A or B (for example, A < WT < B = AB)." [PMID:15833125] subset: PSI-MI_slim synonym: "epistatic" EXACT PSI-MI-short [] synonym: "epistatic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0930 ! epistatic genetic interaction is_a: MI:0931 ! genetic interaction defined by inequality [Term] id: MI:0798 name: conditional genetic interaction defined by inequality namespace: PSI-MI def: "The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab." [PMID:15833125] subset: PSI-MI_slim synonym: "conditional" EXACT PSI-MI-short [] synonym: "conditional genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0931 ! genetic interaction defined by inequality [Term] id: MI:0799 name: additive genetic interaction defined by inequality namespace: PSI-MI def: "Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b." [PMID:15833125] subset: PSI-MI_slim synonym: "additive" EXACT PSI-MI-short [] synonym: "additive genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0931 ! genetic interaction defined by inequality [Term] id: MI:0800 name: single nonmonotonic genetic interaction defined by inequality namespace: PSI-MI def: "The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b." [PMID:15833125] subset: PSI-MI_slim synonym: "single nonmonotonic" EXACT PSI-MI-short [] synonym: "single nonmonotonic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0931 ! genetic interaction defined by inequality [Term] id: MI:0801 name: double nonmonotonic genetic interaction defined by inequality namespace: PSI-MI def: "The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b" [PMID:15833125] subset: PSI-MI_slim synonym: "double nonmonotonic" EXACT PSI-MI-short [] synonym: "double nonmonotonic genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0931 ! genetic interaction defined by inequality is_a: MI:0935 ! positive genetic interaction [Term] id: MI:0802 name: enhancement interaction namespace: PSI-MI def: "The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme.\nOBSOLETE: remap to MI:0933 'negative genetic interaction'" [PMID:15833125] subset: PSI-MI_slim synonym: "enhancement" EXACT PSI-MI-short [] is_obsolete: true [Term] id: MI:0803 name: expression level alteration namespace: PSI-MI def: "Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell." [PMID:14755292] subset: PSI-MI_slim synonym: "expression modif" EXACT PSI-MI-short [] is_a: MI:0787 ! genetic experimental form [Term] id: MI:0804 name: mutated gene namespace: PSI-MI def: "The gene is mutated in some unknown manner" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0787 ! genetic experimental form [Term] id: MI:0805 name: wwpdb namespace: PSI-MI def: "The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.\nhttp://www.wwpdb.org/" [PMID:14634627] subset: Drugable subset: PSI-MI_slim synonym: "wwPDB" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\" is_a: MI:0447 ! feature database is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0806 name: pdbj namespace: PSI-MI def: "PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites.\nhttp://www.pdbj.org/" [PMID:12099029] subset: PSI-MI_slim synonym: "PDBj" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\][a-zA-Z0-9\]\{3}\" xref: search-url: "http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet?PDBID=${ac}&PAGEID=Summary" is_a: MI:0805 ! wwpdb [Term] id: MI:0807 name: comigration in gel electrophoresis namespace: PSI-MI def: "The interaction of two molecules is determine by their very close proximity or the overlap of their relative bands in a gel." [PMID:14755292] subset: PSI-MI_slim synonym: "comigration in gel" EXACT PSI-MI-short [] is_a: MI:0982 ! electrophoretic mobility-based method [Term] id: MI:0808 name: comigration in sds page namespace: PSI-MI def: "Method allowing the detection of strong interactions between two molecules by their very close proximity or the overlap of their relative bands in a denaturing SDS gel." [PMID:14755292, PMID:16732283] subset: PSI-MI_slim synonym: "comigration in sds" EXACT PSI-MI-short [] is_a: MI:0807 ! comigration in gel electrophoresis [Term] id: MI:0809 name: bimolecular fluorescence complementation namespace: PSI-MI alt_id: MI:0229 def: "The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy." [PMID:11983170] subset: PSI-MI_slim synonym: "bifc" EXACT PSI-MI-short [] synonym: "gfp complementation" EXACT [] synonym: "green fluorescence protein complementation assay" EXACT [] is_a: MI:0051 ! fluorescence technology is_a: MI:0090 ! protein complementation assay [Term] id: MI:0810 name: substitution analysis namespace: PSI-MI def: "In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "substitut analysis" EXACT PSI-MI-short [] is_a: MI:0074 ! mutation analysis [Term] id: MI:0811 name: insertion analysis namespace: PSI-MI def: "In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0074 ! mutation analysis [Term] id: MI:0812 name: calmodulin binding protein tag namespace: PSI-MI def: "The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin." [PMID:14755292] subset: PSI-MI_slim synonym: "cam tag" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0813 name: proximity enzyme linked immunosorbent assay namespace: PSI-MI def: "Method allowing efficient and precise interaction detection, along with extensive repertoires of specific binding reagents. It is based on proximity a ligation mechanism that enables sensitive high-capacity protein measurements by converting the detection of specific proteins to the analysis of DNA sequences. Proximity probes containing oligonucleotide extensions are designed to bind pairwise to target proteins and to form amplifiable tag sequences by ligation when brought in proximity." [PMID:15155907, PMID:\:17072308] subset: PSI-MI_slim synonym: "p elisa" EXACT PSI-MI-short [] synonym: "pELISA" EXACT PSI-MI-alternate [] synonym: "pLISA" RELATED [] synonym: "proximity ligation" RELATED [] is_a: MI:0400 ! affinity technology is_a: MI:0421 ! identification by antibody [Term] id: MI:0814 name: protease accessibility laddering namespace: PSI-MI def: "In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis)." [PMID:16615907] subset: PSI-MI_slim synonym: "pal" EXACT PSI-MI-alternate [] synonym: "protease access" EXACT PSI-MI-short [] is_a: MI:0605 ! enzymatic footprinting [Term] id: MI:0815 name: confirmation by molecular weight namespace: PSI-MI def: "Molecule whose sequence identity is derived from their molecular weight" [PMID:14755292] subset: PSI-MI_slim synonym: "weight identificat" EXACT PSI-MI-short [] is_a: MI:0396 ! predetermined participant [Term] id: MI:0816 name: molecular weight estimation by staining namespace: PSI-MI def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker." [PMID:14755292] subset: PSI-MI_slim synonym: "weight by staining" EXACT PSI-MI-short [] is_a: MI:0815 ! confirmation by molecular weight [Term] id: MI:0817 name: molecular weight estimation by silver staining namespace: PSI-MI def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver." [PMID:14755292] subset: PSI-MI_slim synonym: "weight silver stain" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0818 name: molecular weight estimation by coomasie staining namespace: PSI-MI def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye." [PMID:14755292] subset: PSI-MI_slim synonym: "weight by comassie" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0819 name: molecular weight estimation by bromide staining namespace: PSI-MI def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes." [PMID:14755292] subset: PSI-MI_slim synonym: "weight by bromide" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0820 name: molecular weight estimation by sybr staining namespace: PSI-MI def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes." [PMID:14755292] subset: PSI-MI_slim synonym: "safe DNA gel stain" EXACT PSI-MI-alternate [] synonym: "weight by sybr" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0821 name: molecular weight estimation by autoradiography namespace: PSI-MI def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography." [PMID:14755292] subset: PSI-MI_slim synonym: "weight autoradiogra" EXACT PSI-MI-short [] is_a: MI:0815 ! confirmation by molecular weight [Term] id: MI:0822 name: molecular weight estimation by hoechst staining namespace: PSI-MI def: "Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes." [PMID:14755292] subset: PSI-MI_slim synonym: "weight by hoechst" EXACT PSI-MI-short [] is_a: MI:0816 ! molecular weight estimation by staining [Term] id: MI:0823 name: predetermined feature namespace: PSI-MI def: "Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s)." [PMID:14755292] subset: PSI-MI_slim synonym: "predetermined featur" EXACT PSI-MI-short [] is_a: MI:0093 ! protein sequence identification is_a: MI:0427 ! Identification by mass spectrometry is_a: MI:0659 ! experimental feature detection [Term] id: MI:0824 name: x-ray powder diffraction namespace: PSI-MI def: "Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals." [PMID:14755292] subset: PSI-MI_slim synonym: "X-ray" EXACT PSI-MI-alternate [] synonym: "x-ray powder diffrac" EXACT PSI-MI-short [] is_a: MI:0114 ! x-ray crystallography [Term] id: MI:0825 name: x-ray fiber diffraction namespace: PSI-MI def: "Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray." [PMID:14755292] subset: PSI-MI_slim synonym: "X-ray" EXACT PSI-MI-alternate [] synonym: "x-ray fiber diffrac" EXACT PSI-MI-short [] is_a: MI:0114 ! x-ray crystallography [Term] id: MI:0826 name: x ray scattering namespace: PSI-MI def: "Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles." [PMID:14755292] subset: PSI-MI_slim synonym: "saxs" EXACT PSI-MI-short [] is_a: MI:0067 ! light scattering [Term] id: MI:0827 name: x-ray tomography namespace: PSI-MI def: "X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0428 ! imaging technique [Term] id: MI:0828 name: polyprotein fragment namespace: PSI-MI def: "Subpart of a polyprotein that is naturally cleaved in vivo." [PMID:14577292] subset: PSI-MI_slim synonym: "chain" RELATED [] synonym: "polyprotein frag" EXACT PSI-MI-short [] is_a: MI:0252 ! biological feature [Term] id: MI:0829 name: multiple parent reference namespace: PSI-MI def: "This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "multiple parent" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0830 name: tissue list namespace: PSI-MI def: "List of tissue used as topic in UniProt RC line.\nhttp://www.expasy.org/cgi-bin/lists?tisslist.txt" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0473 ! participant database [Term] id: MI:0831 name: cell ontology namespace: PSI-MI def: "Ontology of cell types.\nhttp://obo.sourceforge.net/cgi-bin/detail.cgi?cell" [PMID:16381901] subset: PSI-MI_slim is_a: MI:0473 ! participant database [Term] id: MI:0832 name: half cystine namespace: PSI-MI def: "A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed" [MOD:00798, RESID:AA0025] synonym: "Half of a disulfide bridge" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:0833 name: autoradiography namespace: PSI-MI def: "Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0659 ! experimental feature detection is_a: MI:0866 ! tag visualisation [Term] id: MI:0834 name: ka namespace: PSI-MI def: "Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)" [PMID:14755292] subset: PSI-MI_slim synonym: "kon" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:0835 name: koff namespace: PSI-MI def: "Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)" [PMID:14755292] subset: PSI-MI_slim synonym: "Kd" RELATED [] synonym: "koff" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:0836 name: temperature of interaction namespace: PSI-MI def: "Temperature at which interaction was determined. Unit KELVIN (K)" [PMID:14755292] subset: PSI-MI_slim synonym: "T interaction" EXACT PSI-MI-alternate [] synonym: "temp interaction" EXACT PSI-MI-short [] synonym: "Tint" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0837 name: pH of interaction namespace: PSI-MI def: "pH at which interaction was determined." [PMID:14755292] subset: PSI-MI_slim synonym: "pHint" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:0838 name: kelvin namespace: PSI-MI def: "A scale that measures an object's temperature over absolute zero, the theoretical coolest temperature where all molecular and atomic motion ceases. On the Kelvin scale, the freezing point of water is 273 (273 K = 0 o C = 32 o F)." [PMID:14755292] subset: PSI-MI_slim synonym: "K" EXACT PSI-MI-alternate [] is_a: MI:0647 ! parameter unit [Term] id: MI:0839 name: mole per second namespace: PSI-MI def: "Per mole per second, unit for association rate constant" [PMID:14755292] subset: PSI-MI_slim synonym: "M-1s-1" EXACT PSI-MI-alternate [] is_a: MI:0647 ! parameter unit [Term] id: MI:0840 name: stimulator namespace: PSI-MI def: "Molecule stimulating an interaction by interacting with one or more of the participants." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0500 ! biological role [Term] id: MI:0841 name: phosphotransferase assay namespace: PSI-MI def: "Measures the rate of a phosphate transfer between two molecules." [PMID:14755292] subset: PSI-MI_slim synonym: "phosphotransfer assay" RELATED [] synonym: "phosphotransferase" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study [Term] id: MI:0842 name: phosphate donor namespace: PSI-MI def: "Any molecule that is able to transfer an phosphate to another chemical species." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0918 ! donor [Term] id: MI:0843 name: phosphate acceptor namespace: PSI-MI def: "Molecule to which a phosphate may be transferred from a phosphate donor." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0919 ! acceptor [Term] id: MI:0844 name: phosphotransfer reaction namespace: PSI-MI def: "Reaction where a phosphate is transferred between two proteins of a phosphorelay system. " [PMID:14755292, PMID:16712436] subset: PSI-MI_slim synonym: "phosphotransfer" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0845 name: spin label namespace: PSI-MI def: "Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest." [PMID:10966640] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0846 name: r1 spin label namespace: PSI-MI def: "Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline-\n3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide\nside chain designated R1." [PMID:10966640] subset: PSI-MI_slim is_a: MI:0845 ! spin label [Term] id: MI:0847 name: dansyl tag namespace: PSI-MI def: "Dansyl is fluorescent tag. Dansyl is the acronyme of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups." [PMID:14755292] subset: PSI-MI_slim synonym: "5-dimethylaminonaphthalene-1-sulfonyl tag" EXACT PSI-MI-alternate [] synonym: "dansyl label" EXACT PSI-MI-alternate [] is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0848 name: 125i radiolabel namespace: PSI-MI def: "Molecule labelled with 125 radio isotope of iodine atoms." [PMID:14755292] subset: PSI-MI_slim synonym: "125I" EXACT PSI-MI-alternate [] synonym: "I125" EXACT PSI-MI-alternate [] is_a: MI:0517 ! radiolabel [Term] id: MI:0849 name: ncbi taxonomy namespace: PSI-MI def: "The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available.\nhttp://www.ncbi.nlm.nih.gov/Taxonomy/" [PMID:10592169] subset: PSI-MI_slim xref: id-validation-regexp:\"[0-9\]+\" xref: search-url: "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=${ac}&lvl=3&lin=f&keep=1&srchmode=1&unlock" is_a: MI:0473 ! participant database [Term] id: MI:0850 name: encode namespace: PSI-MI def: "ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project.\nhttp://www.genome.gov/10005107" [PMID:17372197] subset: PSI-MI_slim synonym: "ENCODE" EXACT PSI-MI-alternate [] synonym: "Encyclopedia Of DNA Elements" EXACT PSI-MI-alternate [] is_a: MI:1094 ! genome databases [Term] id: MI:0851 name: protein genbank identifier namespace: PSI-MI def: "GenBank Identifier or GI numbers for proteins." [PMID:17170002] subset: PSI-MI_slim synonym: "GenBank Protein GI" EXACT PSI-MI-alternate [] synonym: "genbank protein gi" EXACT PSI-MI-alternate [] synonym: "genbank_protein_gi" EXACT PSI-MI-short [] synonym: "genpept id" EXACT [] xref: id-validation-regexp:\"[0-9\]+\" xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=Retrieve&dopt=Graphics&list_uids=${ac}" is_a: MI:0860 ! genbank indentifier [Term] id: MI:0852 name: nucleotide genbank identifier namespace: PSI-MI def: "GenBank Identifier or GI numbers for nucleotide." [PMID:17170002] subset: PSI-MI_slim synonym: "genbank nucleotide" EXACT PSI-MI-alternate [] synonym: "GenBank Nucleotide" EXACT PSI-MI-alternate [] synonym: "genbank_nucl_gi" EXACT PSI-MI-short [] xref: id-validation-regexp:\"[0-9\]+\" xref: search-url: "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=Retrieve&dopt=Graphics&list_uids=$" is_a: MI:0860 ! genbank indentifier [Term] id: MI:0853 name: dna overhang namespace: PSI-MI def: "An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase" [PMID:14755292] subset: PSI-MI_slim synonym: "cohessive ends" EXACT PSI-MI-alternate [] synonym: "sticky ends" EXACT PSI-MI-alternate [] is_a: MI:0505 ! experimental feature [Term] id: MI:0854 name: 3 prime overhang namespace: PSI-MI def: "An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "3 prime sticky end" EXACT PSI-MI-alternate [] is_a: MI:0853 ! dna overhang [Term] id: MI:0855 name: 5 prime overhang namespace: PSI-MI def: "An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "5 prime sticky end" EXACT PSI-MI-alternate [] is_a: MI:0853 ! dna overhang [Term] id: MI:0856 name: fluorophore namespace: PSI-MI def: "A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0505 ! experimental feature [Term] id: MI:0857 name: fluorescent dye label namespace: PSI-MI def: "Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescent dye" EXACT PSI-MI-short [] is_a: MI:0856 ! fluorophore [Term] id: MI:0858 name: immunodepleted coimmunoprecipitation namespace: PSI-MI def: "Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex." [PMID:17081976] subset: PSI-MI_slim synonym: "immunodepleted coip" EXACT PSI-MI-alternate [] synonym: "immunodepletion" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation [Term] id: MI:0859 name: intermolecular force namespace: PSI-MI def: "An optical tweezer is a scientific instrument that uses a focused laser beam to provide an attractive or repulsive force, depending on the index mismatch (typically on the order of piconewtons) to physically hold and move microscopic dielectric objects (i.e.highly resistants to the flow of an electric current). This instrument allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies. " [PMID:17023539, PMID:17081984] subset: PSI-MI_slim synonym: "force measurement" EXACT PSI-MI-alternate [] synonym: "molecular force measurement" EXACT PSI-MI-alternate [] synonym: "optical tweezer" EXACT PSI-MI-alternate [] synonym: "single molecule force measurement" EXACT PSI-MI-alternate [] synonym: "surface adhesion force measurement" EXACT PSI-MI-alternate [] is_a: MI:0013 ! biophysical [Term] id: MI:0860 name: genbank indentifier namespace: PSI-MI def: " edit" [PMID:15078858] subset: PSI-MI_slim xref: id-validation-regexp:\"ENS[A-Z\]+[0-9\]\{11}\" is_a: MI:0683 ! sequence database [Term] id: MI:0861 name: protein a tag namespace: PSI-MI def: "The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis." [PMID:14755292] subset: PSI-MI_slim synonym: "protein A" EXACT PSI-MI-alternate [] is_a: MI:0240 ! fusion protein [Term] id: MI:0862 name: zz tag namespace: PSI-MI def: "The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain. " [PMID:11694505] subset: PSI-MI_slim synonym: "ZZ tag" EXACT PSI-MI-alternate [] is_a: MI:0861 ! protein a tag [Term] id: MI:0863 name: thiol reactive lanthanide label namespace: PSI-MI def: "Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attachted to both proteins and DNA." [PMID:10077482] subset: PSI-MI_slim synonym: "Tb3+-DTPA-cs124-EMCH" EXACT PSI-MI-alternate [] synonym: "thiol lanthanide" EXACT PSI-MI-short [] is_a: MI:0505 ! experimental feature [Term] id: MI:0864 name: brenda namespace: PSI-MI def: "A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.\nhttp://www.brenda-enzymes.info" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0473 ! participant database [Term] id: MI:0865 name: fluorescence acceptor donor pair namespace: PSI-MI def: "Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes ." [PMID:14755292] subset: PSI-MI_slim synonym: "fret pair" EXACT PSI-MI-short [] is_a: MI:0495 ! experimental role [Term] id: MI:0866 name: tag visualisation namespace: PSI-MI def: "Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag" [PMID:14755292] subset: PSI-MI_slim is_a: MI:0396 ! predetermined participant [Term] id: MI:0867 name: tag visualisation by fluorescence namespace: PSI-MI def: "The protein is either expressed as a hybrid protein fused to a tag containing a fluorophore, such as green fluorescent protein, or a fluorophore has been chemically attached to the protein. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "tag fluorescence" EXACT PSI-MI-short [] is_a: MI:0866 ! tag visualisation [Term] id: MI:0868 name: author identifier namespace: PSI-MI def: "Author published identifier." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0869 name: originally assigned identifier namespace: PSI-MI def: "Identifier assigned when the record was created by a source database." [PMID:14755292] subset: PSI-MI_slim synonym: "original identifier" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0870 name: demethylase assay namespace: PSI-MI def: "Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study [Term] id: MI:0871 name: demethylation reaction namespace: PSI-MI def: "The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian." [GO:0006482, PMID:17277772] subset: PSI-MI_slim synonym: "demethylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0872 name: atomic force microscopy namespace: PSI-MI def: "The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler.\nhttp://en.wikipedia.org/wiki/Atomic_force_microscope" [PMID:17502105] subset: PSI-MI_slim synonym: "AFM" EXACT PSI-MI-alternate [] synonym: "atomic force microsc" EXACT PSI-MI-short [] is_a: MI:0428 ! imaging technique [Term] id: MI:0873 name: curation request namespace: PSI-MI def: "Annotation of a published paper which has been externally requested." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0875 name: dataset namespace: PSI-MI def: "Targeted curation dataset grouping experiments by topic or dataset origin." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0878 name: author submitted namespace: PSI-MI def: "Data directly submitted by the authors to a database prior to publication." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0665 ! experiment attibute name [Term] id: MI:0879 name: nucleoside triphosphatase assay namespace: PSI-MI def: "Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate." [PMID:14755292] subset: PSI-MI_slim synonym: "triphosphatase ass" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study is_a: MI:0434 ! phosphatase assay [Term] id: MI:0880 name: atpase assay namespace: PSI-MI def: "Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0879 ! nucleoside triphosphatase assay [Term] id: MI:0881 name: nucleoside triphosphatase reaction namespace: PSI-MI def: "Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate." [GO:0017111, PMID:14755292] subset: PSI-MI_slim synonym: "triphosphatase react" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0882 name: atpase reaction namespace: PSI-MI def: "Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate." [GO:0016887, PMID:14755292] subset: PSI-MI_slim is_a: MI:0881 ! nucleoside triphosphatase reaction [Term] id: MI:0883 name: gtpase reaction namespace: PSI-MI def: "Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate." [GO:0003924, PMID:14755292] subset: PSI-MI_slim is_a: MI:0881 ! nucleoside triphosphatase reaction [Term] id: MI:0884 name: vsv tag namespace: PSI-MI def: "Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available." [PMID:14755292] subset: PSI-MI_slim synonym: "vesicular stomatitis virus tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0885 name: journal namespace: PSI-MI def: "Name and details of a journal from which paper has been taken." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0886 name: publication year namespace: PSI-MI def: "Year of publication of a paper." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1093 ! bibliographic attribute name [Term] id: MI:0887 name: histone acetylase assay namespace: PSI-MI def: "In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with \"histone acetyltransferase\" (HAt)" [PMID:14755292] subset: PSI-MI_slim synonym: "HAt" EXACT PSI-MI-alternate [] synonym: "hat" EXACT PSI-MI-short [] synonym: "histone acetylation" RELATED [] is_a: MI:0889 ! acetylase assay [Term] id: MI:0888 name: small angle neutron scattering namespace: PSI-MI def: "During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample." [PMID:11578931] subset: PSI-MI_slim synonym: "SANS" EXACT PSI-MI-alternate [] synonym: "sans" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0889 name: acetylase assay namespace: PSI-MI def: "Measures the catalysis of the addition of an acetyl group to a target molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "acetylation" RELATED [] is_a: MI:0415 ! enzymatic study [Term] id: MI:0890 name: qdot namespace: PSI-MI def: "Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications." [PMID:17569782] subset: PSI-MI_slim is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0891 name: neutron fiber diffraction namespace: PSI-MI def: "Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam." [PMID:10771422, PMID:15272083, PMID:15546977, PMID:15914673, PMID:16041074, PMID:16707576] subset: PSI-MI_slim synonym: "neutron fiber diff" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0892 name: solid phase assay namespace: PSI-MI def: "Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0400 ! affinity technology [Term] id: MI:0893 name: neutron diffraction namespace: PSI-MI def: "Analysis of diffraction pattern using neutron beam" [PMID:10771422, PMID:15272083, PMID:15546977, PMID:15914673, PMID:16041074, PMID:16707576] subset: PSI-MI_slim is_a: MI:0013 ! biophysical [Term] id: MI:0894 name: electron diffraction namespace: PSI-MI def: "Analysis of diffraction pattern using electron beam." [PMID:10949309, PMID:11034202, PMID:11171962, PMID:11532455, PMID:11700061, PMID:15141214, PMID:16325200] subset: PSI-MI_slim is_a: MI:0013 ! biophysical [Term] id: MI:0895 name: protein kinase A complementation namespace: PSI-MI def: "This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA." [PMID:17942691] subset: PSI-MI_slim synonym: "pka complementation" EXACT PSI-MI-short [] is_a: MI:0090 ! protein complementation assay [Term] id: MI:0896 name: renilla luciferase protein tag namespace: PSI-MI def: "Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxigen) that produces light. This protein is often used as a vizualisation tag because compare to many fluorescent tag it has a better signal to noise ratio." [PMID:14755292] subset: PSI-MI_slim synonym: "renilla lucirefase" EXACT PSI-MI-short [] is_a: MI:0240 ! fusion protein [Term] id: MI:0897 name: protein modification ontology namespace: PSI-MI def: "Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue." [PMID:14755292] subset: PSI-MI_slim synonym: "psi-mod" EXACT PSI-MI-short [] xref: id-validation-regexp:\"MOD\:[0-9\]\{5}\" is_a: MI:0447 ! feature database [Term] id: MI:0898 name: putative self namespace: PSI-MI def: "Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer)." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0495 ! experimental role is_a: MI:0500 ! biological role [Term] id: MI:0899 name: p3 filamentous phage display namespace: PSI-MI def: "pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display." [PMID:1696028] subset: PSI-MI_slim synonym: "low valency display" EXACT PSI-MI-alternate [] synonym: "p3 filamentous phage" EXACT PSI-MI-short [] is_a: MI:0048 ! filamentous phage display [Term] id: MI:0900 name: p8 filamentous phage display namespace: PSI-MI def: "pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display." [PMID:1720463] subset: PSI-MI_slim synonym: "high valency display" EXACT PSI-MI-alternate [] synonym: "p8 filamentous phage" EXACT PSI-MI-short [] is_a: MI:0048 ! filamentous phage display [Term] id: MI:0901 name: isotope label footprinting namespace: PSI-MI def: "Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange." [PMID:18184591] subset: PSI-MI_slim synonym: "isotope footprinting" EXACT PSI-MI-short [] is_a: MI:0605 ! enzymatic footprinting [Term] id: MI:0902 name: rna cleavage namespace: PSI-MI def: "Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner." [GO:0006396, PMID:14681407] subset: PSI-MI_slim is_a: MI:0910 ! nucleic acid cleavage [Term] id: MI:0903 name: mpidb namespace: PSI-MI def: "The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions." [PMID:14755292] subset: PSI-MI_slim synonym: "MPDIB" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database [Term] id: MI:0904 name: polysaccharide namespace: PSI-MI def: "A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1100 ! bioactive entity [Term] id: MI:0905 name: amplified luminescent proximity homogeneous assay namespace: PSI-MI def: "AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3)." [PMID:17092917] subset: PSI-MI_slim synonym: "alfa-screen" EXACT PSI-MI-short [] synonym: "AlphaScreen" EXACT PSI-MI-alternate [] is_a: MI:0013 ! biophysical [Term] id: MI:0906 name: au1 tag namespace: PSI-MI def: "The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available." [PMID:18216269] subset: PSI-MI_slim synonym: "DTYRYI epitope tag" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0907 name: conformational status namespace: PSI-MI def: "Statement about the native/denatured conformation of the protein." [PMID:14755292] subset: PSI-MI_slim synonym: "conformation" EXACT PSI-MI-short [] is_a: MI:0346 ! experimental preparation [Term] id: MI:0908 name: denatured namespace: PSI-MI def: "Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0907 ! conformational status [Term] id: MI:0909 name: native namespace: PSI-MI def: "State of the protein without interference i.e. the natural form." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0907 ! conformational status [Term] id: MI:0910 name: nucleic acid cleavage namespace: PSI-MI def: "Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments." [PMID:14755292] subset: PSI-MI_slim synonym: "ncl acid cleavage" EXACT PSI-MI-short [] is_a: MI:0194 ! cleavage reaction [Term] id: MI:0911 name: cross linker namespace: PSI-MI def: "A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed." [PMID:14755292] subset: PSI-MI_slim synonym: "crosslinker" EXACT PSI-MI-alternate [] is_a: MI:0505 ! experimental feature [Term] id: MI:0912 name: spdp cross linker namespace: PSI-MI def: "N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable \nand membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester \nthat will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond." [PMID:17360572] subset: PSI-MI_slim synonym: "N -Succinimidyl 3-(2-pyridyldithio)-propionate" EXACT PSI-MI-alternate [] is_a: MI:0911 ! cross linker [Term] id: MI:0913 name: lc-spdp cross linker namespace: PSI-MI def: "Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable \nand membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester \nthat will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm." [PMID:17360572] subset: PSI-MI_slim synonym: "Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate" EXACT PSI-MI-alternate [] is_a: MI:0912 ! spdp cross linker [Term] id: MI:0914 name: association namespace: PSI-MI def: "Molecules that are experimentally shown to be associated potentially by sharing just one interactor. Often associated molecules are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0190 ! interaction type [Term] id: MI:0915 name: physical association namespace: PSI-MI def: "Molecules that are experimentally shown to belong to the same functional or structural complex." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0914 ! association [Term] id: MI:0916 name: lexa vp16 complementation namespace: PSI-MI def: "Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream." [PMID:9371806] subset: PSI-MI_slim synonym: "lexa vp16 complement" EXACT PSI-MI-short [] synonym: "LexA VP16 transcription complementation" EXACT PSI-MI-alternate [] is_a: MI:0018 ! two hybrid [Term] id: MI:0917 name: matrixdb namespace: PSI-MI def: "Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions." [PMID:19147664] subset: PSI-MI_slim is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database is_a: MI:0973 ! imex source [Term] id: MI:0918 name: donor namespace: PSI-MI def: "Molecule which emits electrons or ions that are transfered to an acceptor molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0500 ! biological role [Term] id: MI:0919 name: acceptor namespace: PSI-MI def: "Molecule able to receive electrons or ions from a donor molecule." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0500 ! biological role [Term] id: MI:0920 name: ribonuclease assay namespace: PSI-MI def: "Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1034 ! nuclease assay [Term] id: MI:0921 name: surface plasmon resonance array namespace: PSI-MI def: "This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot." [PMID:16510109, PMID:16837183, PMID:17889820] subset: PSI-MI_slim synonym: "Biacore Flexchip(r)" EXACT PSI-MI-alternate [] synonym: "spr array" EXACT PSI-MI-short [] synonym: "SPRi-Plex " EXACT PSI-MI-alternate [] synonym: "SPRImager" EXACT PSI-MI-alternate [] is_a: MI:0008 ! array technology is_a: MI:0107 ! surface plasmon resonance [Term] id: MI:0922 name: imex evidence namespace: PSI-MI def: "Experimental evidence supporting an interaction curated and released under the IMEx agreement." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0923 name: irefindex namespace: PSI-MI def: "iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.\nhttp://irefindex.uio.no/" [PMID:18823568] subset: PSI-MI_slim synonym: "iRefIndex" EXACT PSI-MI-alternate [] is_a: MI:0461 ! interaction database is_a: MI:0489 ! source database [Term] id: MI:0924 name: camjedb namespace: PSI-MI def: "Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni.\nhttp://www.sanger.ac.uk/Projects/C_jejuni/" [PMID:106882042] subset: PSI-MI_slim is_a: MI:1094 ! genome databases [Term] id: MI:0925 name: observed ptm namespace: PSI-MI def: "Post translational modification observed on a protein in the context of an interaction." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0668 ! feature attribute name [Term] id: MI:0926 name: fiash label namespace: PSI-MI def: "This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties." [PMID:9657724] subset: PSI-MI_slim synonym: "4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein " EXACT PSI-MI-alternate [] synonym: "FIAsH label" EXACT PSI-MI-alternate [] is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0927 name: iaedans label namespace: PSI-MI def: "IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups." [PMID:11052891] subset: PSI-MI_slim synonym: "(5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) " EXACT PSI-MI-alternate [] synonym: "1,5-IAEDANS" EXACT PSI-MI-alternate [] synonym: "IAEDANS" EXACT PSI-MI-alternate [] is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0928 name: filter trap assay namespace: PSI-MI def: "Biomolecules are mixed in a buffer and the resulting mixture is\npassed through a filter. Large\naggregates are retained on the filter and the pariticipants may then be identified." [PMID:10859365] subset: PSI-MI_slim synonym: "" RELATED [] synonym: "filter binding" EXACT [] synonym: "filter retardation assay" RELATED [] synonym: "Filter retention assay" EXACT PSI-MI-alternate [] synonym: "membrane filtration" RELATED [] is_a: MI:0013 ! biophysical is_a: MI:0091 ! chromatography technology [Term] id: MI:0929 name: northern blot namespace: PSI-MI def: "A standard procedure to identify RNA fragments containing specific\nsequences. In this procedure RNA fragments are separated by\nelectrophoresis, the fragments are transferred to a membrane and the\nmembrane is incubated with a radio labelled probe that hybridises any\ncomplementary subsequence." [PMID:414220] subset: PSI-MI_slim synonym: "northen" EXACT PSI-MI-alternate [] is_a: MI:0078 ! nucleotide sequence identification [Term] id: MI:0930 name: epistatic genetic interaction namespace: PSI-MI def: "The genetic interaction between a group of genes, in which the effects of an allele of one member gene of the group hide the effects of alleles of other genes in the group." [PMID:11988766] subset: PSI-MI_slim synonym: "epistatis" EXACT PSI-MI-short [] is_a: MI:0935 ! positive genetic interaction [Term] id: MI:0931 name: genetic interaction defined by inequality namespace: PSI-MI def: "Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship." [PMID:14755292] subset: PSI-MI_slim synonym: "genetic inequality" EXACT PSI-MI-short [] is_a: MI:0208 ! genetic interaction [Term] id: MI:0932 name: noninteractive genetic interaction defined by inequality namespace: PSI-MI def: "Mutation that has no effect in the WT and b backgrounds, or b has no effect in the a and WT backgrounds, or both hold true. E. g., WT = a > b = ab." [PMID:15833125] subset: PSI-MI_slim synonym: "noninteractive" EXACT PSI-MI-short [] synonym: "noninteractive genetic interaction (sensu inequality)" EXACT PSI-MI-alternate [] is_a: MI:0931 ! genetic interaction defined by inequality is_a: MI:0934 ! neutral genetic interaction [Term] id: MI:0933 name: negative genetic interaction namespace: PSI-MI def: "The phenotype of the double mutant ab is stronger than expected from the combination of the individual effects of a and b." [PMID:14755292] subset: PSI-MI_slim synonym: "negative gen int" EXACT PSI-MI-short [] is_a: MI:0208 ! genetic interaction [Term] id: MI:0934 name: neutral genetic interaction namespace: PSI-MI def: "The phenotype of the double mutant ab is equal to the phenotype expected from the combination of the individual effects of a and b." [PMID:14755292] subset: PSI-MI_slim synonym: "neutral gent int" EXACT PSI-MI-short [] is_a: MI:0208 ! genetic interaction [Term] id: MI:0935 name: positive genetic interaction namespace: PSI-MI def: "The phenotype of the double mutant ab is weaker than expected from the combination of the individual effects of a and b." [PMID:14755292] subset: PSI-MI_slim synonym: "positive gent int" EXACT PSI-MI-short [] is_a: MI:0208 ! genetic interaction [Term] id: MI:0936 name: emdb namespace: PSI-MI def: "The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files." [PMID:14643225] subset: PSI-MI_slim synonym: "Electron Microscopy Data Bank" EXACT PSI-MI-alternate [] synonym: "eMDB" EXACT PSI-MI-short [] is_a: MI:0472 ! pdbe [Term] id: MI:0937 name: glu tag namespace: PSI-MI def: "This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide." [PMID:8077219] subset: PSI-MI_slim synonym: "glu tag" EXACT PSI-MI-short [] is_a: MI:0507 ! tag [Term] id: MI:0938 name: rheology measurement namespace: PSI-MI def: "Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules." [PMID:18445655] subset: PSI-MI_slim synonym: "rheology" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0939 name: fluorescein label namespace: PSI-MI def: "Fluorescence label used to monitor the presence of a protein." [PMID:14755292] subset: PSI-MI_slim synonym: "fluorescein" EXACT PSI-MI-short [] is_a: MI:0857 ! fluorescent dye label [Term] id: MI:0940 name: fluorescein-5-maleimide label namespace: PSI-MI def: "Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions." [PMID:18066077] subset: PSI-MI_slim synonym: "fluor-5-maleimide" EXACT PSI-MI-short [] is_a: MI:0939 ! fluorescein label [Term] id: MI:0941 name: competitor namespace: PSI-MI def: "Binds to the bait molecule in competition with other prey molecules, for example at a shared binding site." [PMID:14755292] subset: PSI-MI_slim synonym: "competitor" EXACT PSI-MI-short [] is_a: MI:0500 ! biological role [Term] id: MI:0942 name: uniprot taxonomy namespace: PSI-MI def: "Based on NCBO Taxonomy but adapted for UniProt\nhttp://www.uniprot.org/taxonomy/" [PMID:18836194] subset: PSI-MI_slim synonym: "uniprot taxon" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[0-9\]+\" xref: search-url: "http://www.uniprot.org/taxonomy/${ac}" is_a: MI:0473 ! participant database [Term] id: MI:0943 name: detection by mass spectrometry namespace: PSI-MI def: "'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer." [PMID:14755292] subset: PSI-MI_slim synonym: "ms interact detect" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical [Term] id: MI:0944 name: mass spectrometry study of hydrogen/deuterium exchange namespace: PSI-MI def: "Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange." [PMID:18948593] subset: PSI-MI_slim synonym: "h1-h2 ms" EXACT PSI-MI-short [] is_a: MI:0943 ! detection by mass spectrometry [Term] id: MI:0945 name: oxidoreductase activity electron transfer reaction namespace: PSI-MI def: "An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced." [GO:GO\:0016491, PMID:14755292] subset: PSI-MI_slim synonym: "redox reaction" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction [Term] id: MI:0946 name: ping namespace: PSI-MI def: "Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay." [PMID:19098921] subset: PSI-MI_slim is_a: MI:0092 ! protein in situ array [Term] id: MI:0947 name: bead aggregation assay namespace: PSI-MI def: "Binding of proteins bound to beads leads to a measurable aggregation of the beads." [PMID:19114658] subset: PSI-MI_slim synonym: "bead aggregation" EXACT PSI-MI-short [] is_a: MI:0892 ! solid phase assay [Term] id: MI:0948 name: kinetic conditions namespace: PSI-MI def: "A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed." [PMID:14755292] subset: PSI-MI_slim synonym: "kinetic_conditions" EXACT PSI-MI-short [] is_a: MI:0664 ! interaction attribute name [Term] id: MI:0949 name: gdp/gtp exchange assay namespace: PSI-MI def: "Experiments monitoring\ninteractions of GTP-GDP exchange factors with their cognate GTPases." [PMID:17925023] subset: PSI-MI_slim synonym: "gdp_gtp exchange" EXACT PSI-MI-short [] synonym: "gtp/gdp exchange" EXACT PSI-MI-alternate [] synonym: "guanine nucleotide exchange assay" EXACT PSI-MI-alternate [] is_a: MI:0401 ! biochemical is_a: MI:1036 ! nucleotide exchange assay [Term] id: MI:0950 name: trapping mutant namespace: PSI-MI def: "Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate." [PMID:9050838] subset: PSI-MI_slim synonym: "trap-mutant" EXACT PSI-MI-short [] is_a: MI:0505 ! experimental feature [Term] id: MI:0951 name: chain parent sequence reference namespace: PSI-MI def: "Reference to the master sequence from which this chain has been derived." [PMID:17925023] subset: PSI-MI_slim synonym: "chain-parent" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type [Term] id: MI:0952 name: imex secondary namespace: PSI-MI def: "Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier." [PMID:17925023] subset: PSI-MI_slim is_a: MI:0353 ! cross-reference type [Term] id: MI:0953 name: polymerization namespace: PSI-MI def: "Interaction inferred by monitoring polymerization/depolymerization of an interactor" [PMID:19081060] subset: PSI-MI_slim synonym: "polymerization" EXACT [] is_a: MI:0401 ! biochemical [Term] id: MI:0954 name: curation quality namespace: PSI-MI def: "An assessment of the depth and extent to which a paper has been curated" [PMID:17893861] subset: PSI-MI_slim relationship: part_of MI:0000 ! molecular interaction [Term] id: MI:0955 name: curation depth namespace: PSI-MI def: "Assessment of the depth to which a paper has been curated" [PMID:17893861] relationship: part_of MI:0954 ! curation quality [Term] id: MI:0956 name: curation coverage namespace: PSI-MI def: "Assessment to the extent of interactions captured in this paper" [PMID:17893861] subset: PSI-MI_slim relationship: part_of MI:0954 ! curation quality [Term] id: MI:0957 name: full coverage namespace: PSI-MI def: "All interactions which can be ascribed to an unambiguous identified in this paper have been captured." [PMID:17893861] subset: PSI-MI_slim is_a: MI:0956 ! curation coverage [Term] id: MI:0958 name: partial coverage namespace: PSI-MI def: "Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured." [PMID:17893861] subset: PSI-MI_slim is_a: MI:0956 ! curation coverage [Term] id: MI:0959 name: imex curation namespace: PSI-MI def: "Paper has been curated to full IMEx specifications" [PMID:17893861] subset: PSI-MI_slim is_a: MI:0955 ! curation depth [Term] id: MI:0960 name: mimix curation namespace: PSI-MI def: "Paper has been curated to meet MIMIx specifications" [PMID:17687370] subset: PSI-MI_slim is_a: MI:0955 ! curation depth [Term] id: MI:0961 name: rapid curation namespace: PSI-MI def: "Minimal interaction data has been extracted from the paper" [PMID:17687370] subset: PSI-MI_slim is_a: MI:0955 ! curation depth [Term] id: MI:0962 name: strep ii tag namespace: PSI-MI def: "The protein of interest is expressed with a StrepII fusion peptide (WSHPQFEK)." [PMID:17571060] subset: PSI-MI_slim synonym: "Strep (II)" EXACT PSI-MI-alternate [] synonym: "Strep II" EXACT PSI-MI-alternate [] is_a: MI:0507 ! tag [Term] id: MI:0963 name: interactome parallel affinity capture namespace: PSI-MI def: "A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press)." [PMID:14681455] synonym: "ipac" EXACT PSI-MI-short [] is_a: MI:0096 ! pull down created_by: orchard creation_date: 2009-05-14T10:56:21Z [Term] id: MI:0964 name: infrared spectroscopy namespace: PSI-MI def: "Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum." [PMID:15212548] subset: PSI-MI_slim synonym: "ir spectrometry" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2009-10-28T10:55:01Z [Term] id: MI:0965 name: 2d-infrared spectrometry namespace: PSI-MI def: "Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles." [PMID:17502604] subset: PSI-MI_slim synonym: "2d-ir" EXACT PSI-MI-short [] is_a: MI:0964 ! infrared spectroscopy created_by: orchard creation_date: 2009-10-28T11:05:01Z [Term] id: MI:0966 name: ultraviolet-visible spectroscopy namespace: PSI-MI def: "Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges." [PMID:18799738] synonym: "ultraviolet-visible spectrophotometry" EXACT [] synonym: "uv-vis" EXACT PSI-MI-short [] synonym: "UV/Vis" EXACT [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2009-10-28T11:12:27Z [Term] id: MI:0967 name: chembl namespace: PSI-MI def: "ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets." [PMID:19194660] subset: Drugable subset: PSI-MI_slim xref: id-validation-regexp:\"[0-9\]+\" xref: search-url:http\://www.ebi.ac.uk/chembldb/index.php/compound/inspect/$(ac) is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2009-10-28T11:20:55Z [Term] id: MI:0968 name: biosensor namespace: PSI-MI def: "A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component" [PMID:10872504] subset: PSI-MI_slim is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2009-10-28T11:44:32Z [Term] id: MI:0969 name: bio-layer interferometry namespace: PSI-MI def: "BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer" [PMID:19561609] subset: PSI-MI_slim synonym: "bli" EXACT PSI-MI-alternate [] is_a: MI:0968 ! biosensor created_by: orchard creation_date: 2009-10-28T11:48:40Z [Term] id: MI:0970 name: inchi key namespace: PSI-MI def: "InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character" [PMID:15889163] subset: Drugable synonym: "inchi key" EXACT PSI-MI-short [] is_a: MI:2010 ! standard inchi created_by: orchard creation_date: 2009-10-28T01:13:25Z [Term] id: MI:0971 name: phosphopantetheinylation namespace: PSI-MI def: "The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine." [PMID:19679086] subset: PSI-MI_slim synonym: "p_patetheinylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2009-10-28T01:20:40Z [Term] id: MI:0972 name: phosphopantetheinylase assay namespace: PSI-MI def: "Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine." [PMID:19346479] synonym: "p_pantethinyl assay" EXACT PSI-MI-short [] synonym: "phosphopantetheinylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2009-10-28T01:23:19Z [Term] id: MI:0973 name: imex source namespace: PSI-MI def: "Databases that contain curated experimental interaction data and exchanging it with other IMEx databases." [PMID:17893861] subset: PSI-MI_slim is_a: MI:0489 ! source database created_by: orchard creation_date: 2009-12-18T10:24:37Z [Term] id: MI:0974 name: innatedb namespace: PSI-MI def: "Human and mouse experimentally verified interactions and pathways involved in innate immunity." [PMID:18766178] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2010-04-09T03:11:54Z [Term] id: MI:0975 name: fc-igg tag namespace: PSI-MI def: "A fusion protein tag consisting of a portion of the constant region of human IgG1." [PMID:11757069] subset: PSI-MI_slim is_a: MI:0240 ! fusion protein created_by: orchard creation_date: 2010-04-21T02:18:04Z [Term] id: MI:0976 name: total internal reflection fluorescence spectroscopy namespace: PSI-MI def: "Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface." [PMID:9013655] subset: PSI-MI_slim synonym: "tirfs" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology created_by: orchard creation_date: 2010-04-21T02:30:46Z [Term] id: MI:0977 name: no-imex-export namespace: PSI-MI def: "Prevents export of experiment and associated interactions to IMEx" [PMID:17893861] subset: PSI-MI_slim is_a: MI:0665 ! experiment attibute name created_by: orchard creation_date: 2010-04-21T02:49:48Z [Term] id: MI:0978 name: author-name namespace: PSI-MI def: "Author given name for a participant, not commonly found in source databases." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0666 ! participant attribute name created_by: orchard creation_date: 2010-04-21T02:55:39Z [Term] id: MI:0979 name: oxidoreductase assay namespace: PSI-MI def: "Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor." [PMID:14755292] subset: PSI-MI_slim synonym: "oxidoreduct assay" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-21T03:04:54Z [Term] id: MI:0980 name: tag visualisation by enzyme assay namespace: PSI-MI def: "The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "tag enzyme assay" EXACT PSI-MI-short [] xref: XX: is_a: MI:0866 ! tag visualisation created_by: orchard creation_date: 2010-04-21T03:18:09Z [Term] id: MI:0981 name: tag visualisation by peroxidase activity namespace: PSI-MI def: "The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequence observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction." [PMID:14755292] subset: PSI-MI_slim synonym: "tag perox activity" EXACT PSI-MI-short [] is_a: MI:0980 ! tag visualisation by enzyme assay created_by: orchard creation_date: 2010-04-21T03:34:14Z [Term] id: MI:0982 name: electrophoretic mobility-based method namespace: PSI-MI def: "Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field." [PMID:19517512] subset: PSI-MI_slim synonym: "electrophoresis" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical created_by: orchard creation_date: 2010-04-26T10:30:36Z [Term] id: MI:0983 name: gemma namespace: PSI-MI def: "GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted\ninto the gas phase by a charged reduced electrospray process. The generated particles, each\ncontaining one protein molecule with a +1 charge, are separated according to size in a differential\nmobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry,\nthis method is run at atmospheric pressure and measures the diameter of the particle rather than the mass." [PMID:16861739] subset: PSI-MI_slim is_a: MI:0982 ! electrophoretic mobility-based method created_by: orchard creation_date: 2010-04-26T10:36:41Z [Term] id: MI:0984 name: deaminase assay namespace: PSI-MI def: "The measurement of the removal of an amine group from a molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "deamination" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T10:45:01Z [Term] id: MI:0985 name: deamination reaction namespace: PSI-MI def: "The removal of an amine group from a molecule." [PMID:14760721] subset: PSI-MI_slim synonym: "deamination" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2010-04-26T10:49:06Z [Term] id: MI:0986 name: nucleic acid strand elongation reaction namespace: PSI-MI def: "The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase." [PMID:159156] subset: PSI-MI_slim synonym: "strand elongation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2010-04-26T10:52:22Z [Term] id: MI:0987 name: rna strand elongation namespace: PSI-MI def: "The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand." [PMID:14755292] subset: PSI-MI_slim synonym: "rna elongation" EXACT PSI-MI-short [] is_a: MI:0986 ! nucleic acid strand elongation reaction created_by: orchard creation_date: 2010-04-26T11:00:08Z [Term] id: MI:0988 name: strep tag namespace: PSI-MI def: "Synthetic peptide consisting of 8 amino acids (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys)." [PMID:17571060, XX:] subset: PSI-MI_slim is_a: MI:0507 ! tag created_by: orchard creation_date: 2010-04-26T11:07:37Z [Term] id: MI:0989 name: amidase assay namespace: PSI-MI def: "The measurement of the addition of an amine group to a molecule." [PMID:14760721] subset: PSI-MI_slim synonym: "amidation" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T11:20:23Z [Term] id: MI:0990 name: cleavage assay namespace: PSI-MI def: "The cleavage of a biomolecule either into its component parts or sub-parts." [PMID:14760721] subset: PSI-MI_slim synonym: "cleavage" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T11:27:22Z [Term] id: MI:0991 name: lipid cleavage assay namespace: PSI-MI def: "The cleavage of a lipid molecule from a larger biomolecule." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0990 ! cleavage assay created_by: orchard creation_date: 2010-04-26T11:30:12Z [Term] id: MI:0992 name: defarnesylase assay namespace: PSI-MI def: "Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue." [PMID:14760721] subset: PSI-MI_slim synonym: "defarnesylation assay" EXACT PSI-MI-short [] is_a: MI:0991 ! lipid cleavage assay created_by: orchard creation_date: 2010-04-26T12:27:47Z [Term] id: MI:0993 name: degeranylase assay namespace: PSI-MI def: "Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue." [PMID:14760721] subset: PSI-MI_slim synonym: "degeranylation assay" EXACT PSI-MI-short [] is_a: MI:0991 ! lipid cleavage assay created_by: orchard creation_date: 2010-04-26T12:36:51Z [Term] id: MI:0994 name: demyristoylase assay namespace: PSI-MI def: "measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue." [PMID:14760721] subset: PSI-MI_slim synonym: "demyristoylation assay" EXACT PSI-MI-short [] is_a: MI:0991 ! lipid cleavage assay created_by: orchard creation_date: 2010-04-26T12:39:30Z [Term] id: MI:0995 name: depalmitoylase assay namespace: PSI-MI def: "Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues." [PMID:14760721] subset: PSI-MI_slim synonym: "depalmitoylation assay" EXACT PSI-MI-short [] is_a: MI:0991 ! lipid cleavage assay created_by: orchard creation_date: 2010-04-26T12:42:00Z [Term] id: MI:0996 name: deformylase assay namespace: PSI-MI def: "Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue." [PMID:14760721] subset: PSI-MI_slim synonym: "deformylase reaction" EXACT PSI-MI-short [] synonym: "deformylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T12:50:38Z [Term] id: MI:0997 name: ubiquitinase assay namespace: PSI-MI def: "Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "ubiquitinase assay" EXACT PSI-MI-short [] synonym: "ubiquitination" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T12:54:02Z [Term] id: MI:0998 name: deubiquitinase assay namespace: PSI-MI def: "Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins." [PMID:14760721] subset: PSI-MI_slim synonym: "deubiquinase assay" RELATED [] synonym: "deubiquitinase assay" EXACT PSI-MI-short [] synonym: "deubiquitination" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T12:56:41Z [Term] id: MI:0999 name: formylase assay namespace: PSI-MI def: "Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:01:44Z [Term] id: MI:1000 name: hydroxylase assay namespace: PSI-MI def: "Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:05:19Z [Term] id: MI:1001 name: lipidase assay namespace: PSI-MI def: "The covalent binding of a lipid group to a peptide chain." [PMID:14760721] subset: PSI-MI_slim synonym: "lipidation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:09:49Z [Term] id: MI:1002 name: myristoylase assay namespace: PSI-MI def: "Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid." [PMID:14707621] subset: PSI-MI_slim synonym: "myristoylation" RELATED [] is_a: MI:1001 ! lipidase assay created_by: orchard creation_date: 2010-04-26T01:16:11Z [Term] id: MI:1003 name: geranylgeranylase assay namespace: PSI-MI def: "Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s)." [PMID:14760721] subset: PSI-MI_slim synonym: "geranylgeranylase" EXACT PSI-MI-short [] synonym: "geranylgeranylation" RELATED [] is_a: MI:1001 ! lipidase assay created_by: orchard creation_date: 2010-04-26T01:20:07Z [Term] id: MI:1004 name: palmitoylase assay namespace: PSI-MI def: "Measurement of the covalent attachment of palmitic acid to a protein." [PMID:14760721] subset: PSI-MI_slim synonym: "myristoylation" RELATED [] synonym: "palmitoylase assay" EXACT PSI-MI-short [] is_a: MI:1001 ! lipidase assay created_by: orchard creation_date: 2010-04-26T01:27:50Z [Term] id: MI:1005 name: adp ribosylase assay namespace: PSI-MI def: "Measurement of the addition of one or more ADP-ribose moieties to molecules." [PMID:14760721] subset: PSI-MI_slim synonym: "adp ribosylase" EXACT PSI-MI-short [] synonym: "adp ribosylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:30:24Z [Term] id: MI:1006 name: deglycosylase assay namespace: PSI-MI def: "Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:34:07Z [Term] id: MI:1007 name: glycosylase assay namespace: PSI-MI def: "Measurement of the covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer." [PMID:14760721] subset: PSI-MI_slim synonym: "glycosylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:35:37Z [Term] id: MI:1008 name: sumoylase assay namespace: PSI-MI def: "Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "sumoylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:37:31Z [Term] id: MI:1009 name: desumoylase assay namespace: PSI-MI def: "Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "desumylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:38:56Z [Term] id: MI:1010 name: neddylase assay namespace: PSI-MI def: "Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "neddylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:41:40Z [Term] id: MI:1011 name: deneddylase assay namespace: PSI-MI def: "Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target." [PMID:14760721] subset: PSI-MI_slim synonym: "deneddylation" RELATED [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-04-26T01:42:49Z [Term] id: MI:1012 name: sbp namespace: PSI-MI def: "38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide." [PMID:117222181] subset: PSI-MI_slim synonym: "steptavidin binding peptide" RELATED [] is_a: MI:0507 ! tag created_by: orchard creation_date: 2010-04-29T08:42:26Z [Term] id: MI:1013 name: ensemblgenomes namespace: PSI-MI def: "Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range.\nhttp://www.ensemblgenomes.org" [PMID:19884133] subset: PSI-MI_slim is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2010-05-06T08:09:20Z [Term] id: MI:1014 name: string namespace: PSI-MI def: "STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins." [PMID:18940858] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2010-07-15T11:00:57Z [Term] id: MI:1015 name: dictybase namespace: PSI-MI def: "dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome." [] subset: PSI-MI_slim xref: id-validation-regexp:\"DDB_G(0-9)\{7}\" is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2010-07-29T01:19:40Z [Term] id: MI:1016 name: fluorescence recovery after photobleaching namespace: PSI-MI def: "Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction." [PMID:15695095, PMID:17711354] subset: PSI-MI_slim synonym: "" RELATED [] synonym: "frap" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology created_by: orchard creation_date: 2010-11-11T10:39:37Z [Term] id: MI:1017 name: rna immunoprecipitation namespace: PSI-MI def: "Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR." [PMID:18265380] subset: PSI-MI_slim synonym: "rip" RELATED [] synonym: "rna-ip" EXACT PSI-MI-short [] is_a: MI:0019 ! coimmunoprecipitation created_by: orchard creation_date: 2010-11-11T10:58:47Z [Term] id: MI:1018 name: deltamass namespace: PSI-MI def: "A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home" [PMID:8322616] subset: PSI-MI_slim is_a: MI:0447 ! feature database created_by: orchard creation_date: 2010-11-11T11:04:13Z [Term] id: MI:1019 name: protein phosphatase assay namespace: PSI-MI def: "Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate." [] subset: PSI-MI_slim is_a: MI:0434 ! phosphatase assay created_by: orchard creation_date: 2010-11-11T11:30:47Z [Term] id: MI:1020 name: hilyte fluor 488 namespace: PSI-MI def: "A carbonyl-reactive fluorescent labelling dye." [PMID:19795889] subset: PSI-MI_slim synonym: "hilyte 488" EXACT PSI-MI-short [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2010-11-11T11:35:48Z [Term] id: MI:1021 name: qx 520 namespace: PSI-MI def: "Nonfluorescent dye, act as a quencher in FRET assays." [] subset: PSI-MI_slim is_a: MI:0373 ! dye label created_by: orchard creation_date: 2010-11-11T11:40:16Z [Term] id: MI:1022 name: field flow fractionation namespace: PSI-MI def: "A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids." [PMID:959835] subset: PSI-MI_slim is_a: MI:0027 ! cosedimentation created_by: orchard creation_date: 2010-11-11T11:55:40Z [Term] id: MI:1023 name: luminogreen namespace: PSI-MI def: "A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell." [PMID:19935683] subset: PSI-MI_slim is_a: MI:0373 ! dye label created_by: orchard creation_date: 2010-11-11T12:10:26Z [Term] id: MI:1024 name: scanning electron microscopy namespace: PSI-MI def: "A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity." [PMID:20463740] subset: PSI-MI_slim synonym: "sem" EXACT PSI-MI-alternate [] is_a: MI:0040 ! electron microscopy created_by: orchard creation_date: 2010-11-11T12:17:54Z [Term] id: MI:1025 name: unimod namespace: PSI-MI def: "A database of protein modifications for mass spectrometry. www.unimod.org" [PMID:15174123] is_a: MI:0447 ! feature database created_by: orchard creation_date: 2010-11-11T12:24:10Z [Term] id: MI:1026 name: diphtamidase assay namespace: PSI-MI def: "Measurement of a modification that converts an L-histidine residue to diphthamide." [PMID:14760721] subset: PSI-MI_slim synonym: "diphtamidase" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-11-11T12:33:29Z [Term] id: MI:1027 name: diphtamidation reaction namespace: PSI-MI def: "A modification that converts an L-histidine residue to diphthamide." [PMID:14760721] subset: PSI-MI_slim synonym: "diphthamidation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2010-11-11T12:36:51Z [Term] id: MI:1028 name: modified chromatin immunoprecipitation namespace: PSI-MI def: "Chromatin-bound protein networks isolated using magnetic beads coated with antibodies." [PMID:19106085] subset: PSI-MI_slim synonym: "mch-ip" EXACT PSI-MI-short [] is_a: MI:0402 ! chromatin immunoprecipitation assay created_by: orchard creation_date: 2010-11-11T12:58:52Z [Term] id: MI:1029 name: proteomics of isolated chromatin segments namespace: PSI-MI def: "Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified." [PMID:19135898] subset: PSI-MI_slim synonym: "pich" EXACT PSI-MI-alternate [] is_a: MI:0402 ! chromatin immunoprecipitation assay created_by: orchard creation_date: 2010-11-11T01:03:21Z [Term] id: MI:1030 name: excimer fluorescence namespace: PSI-MI def: "Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule." [PMID:18480256] subset: PSI-MI_slim synonym: "excimer fluoresc" EXACT PSI-MI-short [] is_a: MI:0051 ! fluorescence technology created_by: orchard creation_date: 2010-11-11T01:15:19Z [Term] id: MI:1031 name: protein folding/unfolding namespace: PSI-MI def: "A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding." [PMID:19940245] subset: PSI-MI_slim synonym: "protein folding" EXACT PSI-MI-short [] is_a: MI:0400 ! affinity technology created_by: orchard creation_date: 2010-11-11T01:24:11Z [Term] id: MI:1032 name: atto 488 namespace: PSI-MI def: "Fluorescent tag - maleimide couples to thiols." [PMID:14760721] subset: PSI-MI_slim synonym: "atto 488 maleimide" EXACT [] synonym: "atto488" RELATED [] is_a: MI:1092 ! atto label created_by: orchard creation_date: 2010-11-11T01:33:13Z [Term] id: MI:1033 name: atto 550 namespace: PSI-MI def: "Fluorescent tag - maleimide couples to thiols." [PMID:14760721] subset: PSI-MI_slim synonym: "atto550" RELATED [] is_a: MI:1092 ! atto label created_by: orchard creation_date: 2010-11-11T01:39:43Z [Term] id: MI:1034 name: nuclease assay namespace: PSI-MI def: "Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids." [PMID:14760721] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2010-11-11T01:43:11Z [Term] id: MI:1035 name: deoxyribonuclease assay namespace: PSI-MI def: "Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA." [PMID:14760721] subset: PSI-MI_slim synonym: "deoxyribonuclease" EXACT PSI-MI-short [] is_a: MI:1034 ! nuclease assay created_by: orchard creation_date: 2010-11-11T01:45:29Z [Term] id: MI:1036 name: nucleotide exchange assay namespace: PSI-MI def: "Experiments monitoring\ninteractions of nucleotide exchange factors with their cognate nucleotidases." [PMID:14760721] subset: PSI-MI_slim synonym: "nucleotide exchange" EXACT PSI-MI-short [] is_a: MI:0401 ! biochemical created_by: orchard creation_date: 2010-11-11T01:54:00Z [Term] id: MI:1037 name: Split renilla luciferase complementation namespace: PSI-MI def: "The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light." [PMID:12705589] subset: PSI-MI_slim synonym: "renilla luciferase" EXACT PSI-MI-alternate [] is_a: MI:0090 ! protein complementation assay created_by: orchard creation_date: 2010-11-11T02:54:08Z [Term] id: MI:1038 name: silicon nanowire field-effect transistor namespace: PSI-MI def: "Measures selective electrical response to molecules binding to the immobilised bait." [PMID:20080536] subset: PSI-MI_slim synonym: "nanowire transistor" EXACT PSI-MI-alternate [] is_a: MI:0968 ! biosensor created_by: orchard creation_date: 2010-11-11T03:11:33Z [Term] id: MI:1039 name: c-terminal range namespace: PSI-MI def: "The C-terminal region of a sequence, exact coordinates not available." [PMID:14760721] subset: PSI-MI_slim synonym: "" RELATED [] synonym: "c-term range" EXACT PSI-MI-short [] is_a: MI:0333 ! feature range status created_by: orchard creation_date: 2010-11-11T03:20:34Z [Term] id: MI:1040 name: n-terminal range namespace: PSI-MI def: "The N-terminal region of a sequence, exact coordinates not available." [PMID:14760721] subset: PSI-MI_slim synonym: "n-term range" EXACT PSI-MI-short [] is_a: MI:0333 ! feature range status created_by: orchard creation_date: 2010-11-11T03:27:57Z [Term] id: MI:1041 name: synonym namespace: PSI-MI def: "Alternative name or descriptor for an entity." [PMID:14681455] subset: PSI-MI_slim is_a: MI:0300 ! alias type created_by: orchard creation_date: 2010-12-02T10:26:35Z [Term] id: MI:1042 name: pubmed central namespace: PSI-MI def: "PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals." [PMID:12519941] subset: PSI-MI_slim synonym: "14755292] subset: PSI-MI_slim is_a: MI:1050 ! interaction representation created_by: orchard creation_date: 2011-03-11T01:27:00Z [Term] id: MI:1052 name: clustered namespace: PSI-MI def: "Binary pair is defined by multiple pieces of experimental evidence which have been clustered together." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1050 ! interaction representation created_by: orchard creation_date: 2011-03-11T01:28:50Z [Term] id: MI:1053 name: data source namespace: PSI-MI def: "The source of the data entered into the database." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1045 ! curation content created_by: orchard creation_date: 2011-03-11T01:32:16Z [Term] id: MI:1054 name: experimentally-observed namespace: PSI-MI def: "Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:33:48Z [Term] id: MI:1055 name: internally-curated namespace: PSI-MI def: "Data has been directly curated into this database from the paper describing the experimental evidence" [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:35:12Z [Term] id: MI:1056 name: text-mining namespace: PSI-MI def: "The data has been entered into the database following extraction from the literature by a computational process." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:36:34Z [Term] id: MI:1057 name: predicted namespace: PSI-MI def: "The interaction has been predicted using a specific algorithm." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:37:47Z [Term] id: MI:1058 name: imported namespace: PSI-MI def: "The data has been imported into the database form an external resource." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1053 ! data source created_by: orchard creation_date: 2011-03-11T01:39:23Z [Term] id: MI:1059 name: complex expansion namespace: PSI-MI def: "The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1045 ! curation content created_by: orchard creation_date: 2011-03-11T01:41:16Z [Term] id: MI:1060 name: spoke expansion namespace: PSI-MI def: "Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1059 ! complex expansion created_by: orchard creation_date: 2011-03-11T01:42:35Z [Term] id: MI:1061 name: matrix expansion namespace: PSI-MI def: "Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1059 ! complex expansion created_by: orchard creation_date: 2011-03-11T01:45:52Z [Term] id: MI:1062 name: bipartite expansion namespace: PSI-MI def: "Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity." [PMID:14755292] subset: PSI-MI_slim is_a: MI:1059 ! complex expansion created_by: orchard creation_date: 2011-03-11T01:49:08Z [Term] id: MI:1063 name: consensuspathdb namespace: PSI-MI def: "ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided." [PMID:21071422] subset: PSI-MI_slim is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-06-21T02:40:16Z [Term] id: MI:1064 name: interaction confidence namespace: PSI-MI def: "A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction." [PMID:19420069] subset: PSI-MI_slim synonym: "confidence" EXACT PSI-MI-short [] synonym: "scoring system" EXACT [] relationship: part_of MI:0000 ! molecular interaction created_by: orchard creation_date: 2011-07-05T07:13:57Z [Term] id: MI:1065 name: replication-based confidence namespace: PSI-MI def: "Methods based on counting the number of replicates in which an interaction has been observed." [PMID:19420069] subset: PSI-MI_slim synonym: "replication score" EXACT PSI-MI-alternate [] synonym: "replication-based scoring system" RELATED [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:22:02Z [Term] id: MI:1066 name: structure-based confidence namespace: PSI-MI def: "Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc." [PMID:15044803] subset: PSI-MI_slim synonym: "structure score" EXACT PSI-MI-alternate [] synonym: "structure-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:38:50Z [Term] id: MI:1067 name: function-based confidence namespace: PSI-MI def: "Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms." [PMID:21443973] subset: PSI-MI_slim synonym: "function score" EXACT PSI-MI-short [] synonym: "function-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:46:28Z [Term] id: MI:1068 name: location-based confidence namespace: PSI-MI def: "Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues." [PMID:18624398] subset: PSI-MI_slim synonym: "colocation score" EXACT PSI-MI-short [] synonym: "location-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:52:36Z [Term] id: MI:1069 name: network-based confidence namespace: PSI-MI def: "Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison\nwith genetic interactions." [PMID:19010802] subset: PSI-MI_slim synonym: "network score" EXACT PSI-MI-short [] synonym: "network-based scoring system" EXACT PSI-MI-short [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T07:59:13Z [Term] id: MI:1070 name: standard-based confidence namespace: PSI-MI def: "Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules." [PMID:16554755] subset: PSI-MI_slim synonym: "gold standard" RELATED [] synonym: "standard score" EXACT PSI-MI-short [] synonym: "standard-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T08:09:46Z [Term] id: MI:1071 name: literature-based confidence namespace: PSI-MI def: "Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining." [PMID:18005433] subset: PSI-MI_slim synonym: "literature score" EXACT PSI-MI-short [] synonym: "literature-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T08:24:46Z [Term] id: MI:1072 name: method-based confidence namespace: PSI-MI def: "The confidence of an interaction is assessed on the number of different methods by which it is observed." [PMID:19420069] subset: PSI-MI_slim synonym: "method score" EXACT PSI-MI-short [] synonym: "method-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T08:42:47Z [Term] id: MI:1073 name: statistical-based confidence namespace: PSI-MI def: "Confidence in an interaction is based on a measure of the probability of these molecules interacting." [PMID:19420069] subset: PSI-MI_slim synonym: "statistical score" EXACT PSI-MI-short [] synonym: "statistical-based scoring system" EXACT [] is_a: MI:1064 ! interaction confidence created_by: orchard creation_date: 2011-07-05T08:50:05Z [Term] id: MI:1074 name: rgs-his tag namespace: PSI-MI def: "The protein of interest is expressed as a fusion to a RGS(His)n tag." [PMID:19223579] synonym: "rgs-his" EXACT PSI-MI-short [] is_a: MI:0521 ! his tag created_by: orchard creation_date: 2011-07-05T09:52:28Z [Term] id: MI:1075 name: beilstein namespace: PSI-MI def: "The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number." [PMID:ID\:11604014] subset: PSI-MI_slim synonym: "beilstein" EXACT PSI-MI-short [] is_a: MI:2054 ! bioactive entity reference created_by: orchard creation_date: 2011-07-05T10:03:13Z [Term] id: MI:1076 name: einecs namespace: PSI-MI def: "The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets." [PMID:17125194] subset: PSI-MI_slim synonym: "einecs" EXACT PSI-MI-short [] synonym: "European Inventory of Existing Commercial Chemical Substances " EXACT [] is_a: MI:2054 ! bioactive entity reference created_by: orchard creation_date: 2011-07-05T10:09:35Z [Term] id: MI:1077 name: merck index namespace: PSI-MI def: "Comprehensive information on chemicals, drugs, and biologicals." [PMID:17832605] subset: PSI-MI_slim synonym: "merck index" EXACT PSI-MI-short [] is_a: MI:2054 ! bioactive entity reference created_by: orchard creation_date: 2011-07-05T10:15:56Z [Term] id: MI:1078 name: plantgdb namespace: PSI-MI def: "PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities." [PMID:18063570] subset: PSI-MI_slim synonym: "plantgdb" EXACT PSI-MI-short [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:27:50Z [Term] id: MI:1079 name: ratmap namespace: PSI-MI def: "The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap." [PMID:15608244] subset: PSI-MI_slim synonym: "ratmap" EXACT PSI-MI-short [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:32:10Z [Term] id: MI:1080 name: tair namespace: PSI-MI def: "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community." [PMID:20521243] subset: PSI-MI_slim synonym: "tair" EXACT PSI-MI-short [] synonym: "The Arabidopsis Information Resource" EXACT [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:34:26Z [Term] id: MI:1081 name: tigr/jcvi namespace: PSI-MI def: "The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR)." [PMID:18287690] subset: PSI-MI_slim synonym: "J. Craig Venter Institute" EXACT [] synonym: "The Institute for Genomic Research" EXACT PSI-MI-short [] synonym: "tigr/jcvi" EXACT PSI-MI-short [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:44:11Z [Term] id: MI:1082 name: zfin namespace: PSI-MI def: "Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools." [PMID:21036866] synonym: "The Zebrafish Model Organism Database " EXACT [] synonym: "zfin" EXACT PSI-MI-short [] is_a: MI:1094 ! genome databases created_by: orchard creation_date: 2011-07-05T10:53:21Z [Term] id: MI:1083 name: cog namespace: PSI-MI def: "Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain." [PMID:11125040] subset: PSI-MI_slim synonym: "Clusters of Orthologous Groups" EXACT [] synonym: "cogg" EXACT PSI-MI-short [] is_a: MI:0447 ! feature database created_by: orchard creation_date: 2011-07-05T10:59:06Z [Term] id: MI:1084 name: photon donor namespace: PSI-MI def: "Any molecule that is able to transfer a photon to another chemical species." [PMID:14755292] subset: PSI-MI_slim synonym: "photon donor" EXACT PSI-MI-short [] is_a: MI:0918 ! donor created_by: orchard creation_date: 2011-07-05T11:03:38Z [Term] id: MI:1085 name: photon acceptor namespace: PSI-MI def: "Molecule to which a photon may be transferred from an photon donor." [PMID:14755292] subset: PSI-MI_slim synonym: "photon acceptor" EXACT PSI-MI-short [] is_a: MI:0919 ! acceptor created_by: orchard creation_date: 2011-07-05T11:06:47Z [Term] id: MI:1086 name: equilibrium dialysis namespace: PSI-MI def: "Two chambers are separated by a dialysis membrane. The molecular weight cut off\n(MWCO) of this membrane is\nchosen such that it will retain the\nreceptor component of the sample\n(the element which will bind\nthe ligand).\nA known concentration and volume\nof ligand is placed into one of\nthe chambers. The ligand is small\nenough to pass freely through the\nmembrane.\nA known concentration of receptor\nis then placed in the remaining\nchamber in an equivalent volume\nto that placed in the first chamber.\nAs the ligand diffuses across the\nmembrane some of it will bind to\nthe receptor and some will remain\nfree in solution. The higher the\naffinity of the interaction, the higher\nthe concentration of ligand that\nwill be bound at any time." [PMID:21609686] synonym: "equilib. dialysis" EXACT PSI-MI-short [] is_a: MI:0013 ! biophysical created_by: orchard creation_date: 2011-07-05T11:12:25Z [Term] id: MI:1087 name: monoclonal antibody blockade namespace: PSI-MI def: "Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule." [PMID:14755292] subset: PSI-MI_slim synonym: "mab blockade" EXACT PSI-MI-short [] is_a: MI:0400 ! affinity technology created_by: orchard creation_date: 2011-07-05T11:19:37Z [Term] id: MI:1088 name: phenotype-based detection assay namespace: PSI-MI def: "Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor." [PMID:14755292] synonym: "phenotype-based" EXACT PSI-MI-short [] is_a: MI:0045 ! experimental interaction detection created_by: orchard creation_date: 2011-07-05T11:24:37Z [Term] id: MI:1089 name: nuclear translocation assay namespace: PSI-MI def: "Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules." [PMID:21684252] subset: PSI-MI_slim synonym: "nuclear translocation" EXACT PSI-MI-short [] is_a: MI:1088 ! phenotype-based detection assay created_by: orchard creation_date: 2011-07-05T11:27:16Z [Term] id: MI:1090 name: bimane label namespace: PSI-MI def: "Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione." [PMID:7378449] subset: PSI-MI_slim synonym: "bimane" EXACT PSI-MI-short [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2011-07-05T12:03:52Z [Term] id: MI:1091 name: publication title namespace: PSI-MI def: "Title of the publication." [PMID:14755292] subset: PSI-MI_slim synonym: "title" EXACT PSI-MI-short [] is_a: MI:1093 ! bibliographic attribute name created_by: orchard creation_date: 2011-07-05T12:07:49Z [Term] id: MI:1092 name: atto label namespace: PSI-MI def: "Fluorescent dyes - spectral range 500 to 700 nm." [PMID:14755292] synonym: "atto label" EXACT PSI-MI-short [] is_a: MI:0857 ! fluorescent dye label created_by: orchard creation_date: 2011-07-05T12:14:52Z [Term] id: MI:1093 name: bibliographic attribute name namespace: PSI-MI def: "Attributes specific to the publication." [PMID:14755292] subset: PSI-MI_slim synonym: "bib attribute" EXACT PSI-MI-short [] synonym: "publication attribute" EXACT [] is_a: MI:0665 ! experiment attibute name created_by: orchard creation_date: 2011-07-05T12:55:21Z [Term] id: MI:1094 name: genome databases namespace: PSI-MI def: "Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences." [PMID:14755292] subset: PSI-MI_slim synonym: "genome databases" EXACT PSI-MI-short [] is_a: MI:0683 ! sequence database created_by: orchard creation_date: 2011-07-06T07:57:46Z [Term] id: MI:1095 name: hgnc namespace: PSI-MI def: "HGNC is the nomenclature committee responsible for the naming of human genes." [PMID:20929869] synonym: "hgnc" EXACT PSI-MI-short [] synonym: "Human Genome Nomenclature Committee" EXACT PSI-MI-short [] is_a: MI:1109 ! gene database created_by: orchard creation_date: 2011-07-06T08:02:03Z [Term] id: MI:1096 name: protein sequence databases namespace: PSI-MI def: "Databases dedicated to the collection and annotation of protein sequences." [PMID:21447597] subset: PSI-MI_slim synonym: "protein seq db" EXACT PSI-MI-short [] is_a: MI:0683 ! sequence database created_by: orchard creation_date: 2011-07-06T08:10:40Z [Term] id: MI:1097 name: uniprot namespace: PSI-MI def: "UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation." [PMID:21051339] subset: PSI-MI_slim synonym: "uniprot" EXACT PSI-MI-short [] is_a: MI:1096 ! protein sequence databases created_by: orchard creation_date: 2011-07-06T08:14:40Z [Term] id: MI:1098 name: uniprot/swiss-prot namespace: PSI-MI def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.\nhttp://www.uniprot.org. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator" [PMID:14681372, PMID:21447597] subset: PSI-MI_slim synonym: "swiss-prot" EXACT PSI-MI-short [] synonym: "UniProt" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]|[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]-[0-9\]+|[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]-PRO_[0-9\]\{10}\" xref: search-url: "http://www.uniprot.org/uniprot/{ac}" is_a: MI:0486 ! uniprot knowledge base created_by: orchard creation_date: 2011-07-06T08:17:34Z [Term] id: MI:1099 name: uniprot/trembl namespace: PSI-MI def: "UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.\nhttp://www.uniprot.org. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification." [PMID:14681372, PMID:21447597] subset: PSI-MI_slim synonym: "trembl" EXACT PSI-MI-short [] synonym: "UniProt" EXACT PSI-MI-alternate [] xref: id-validation-regexp:\"[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]|[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]-[0-9\]+|[A-Z\][0-9\][A-Z0-9\]\{3}[0-9\]-PRO_[0-9\]\{10}\" xref: search-url: "http://www.uniprot.org/uniprot/{ac}" is_a: MI:0486 ! uniprot knowledge base created_by: orchard creation_date: 2011-07-06T08:20:24Z [Term] id: MI:1100 name: bioactive entity namespace: PSI-MI def: "Molecules showing activity in a living system but not encoded by a genomic sequence." [PMID:14760721] synonym: "bioactive entity" EXACT PSI-MI-short [] is_a: MI:0313 ! interactor type created_by: orchard creation_date: 2011-07-06T08:23:48Z [Term] id: MI:1101 name: standard inchi key namespace: PSI-MI def: "The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes)" [PMC:2867152] synonym: "standard inchi key" EXACT PSI-MI-short [] synonym: "standard inchikey" EXACT PSI-MI-short [] is_a: MI:0970 ! inchi key created_by: orchard creation_date: 2011-07-06T09:02:25Z [Term] id: MI:1102 name: mapped-identity namespace: PSI-MI def: "Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database." [PMID:14760721] synonym: "mapped-identity" EXACT PSI-MI-short [] is_a: MI:0353 ! cross-reference type created_by: orchard creation_date: 2011-07-06T09:07:02Z [Term] id: MI:1103 name: solution state nmr namespace: PSI-MI def: "NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp\ntransitions, due to averaging of anisotropic NMR interactions\nby rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations." [PMID:20951674] subset: PSI-MI_slim synonym: "solution state nmr" EXACT [] synonym: "soultion nmr" EXACT PSI-MI-short [] is_a: MI:0077 ! nuclear magnetic resonance created_by: orchard creation_date: 2011-07-06T09:16:45Z [Term] id: MI:1104 name: solid state nmr namespace: PSI-MI def: "Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full\neffects of anisotropic or orientation-dependent interactions are observed in the spectrum." [PMID:20951674] subset: PSI-MI_slim synonym: "solid state nmr" EXACT PSI-MI-short [] synonym: "ssnmr" EXACT [] is_a: MI:0077 ! nuclear magnetic resonance created_by: orchard creation_date: 2011-07-06T09:23:11Z [Term] id: MI:1105 name: biocyc namespace: PSI-MI def: "BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/)." [PMID:19850718] subset: PSI-MI_slim synonym: "biocyc" EXACT PSI-MI-short [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-07-06T09:43:03Z [Term] id: MI:1106 name: pathways database namespace: PSI-MI def: "Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways." [PMID:14755292] subset: PSI-MI_slim synonym: "pathways db" EXACT PSI-MI-short [] is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-07-07T02:52:18Z [Term] id: MI:1107 name: pid namespace: PSI-MI def: "Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/)." [PMID:18832364] synonym: "pathways interaction database" EXACT [] synonym: "pid" EXACT PSI-MI-short [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-07-07T03:00:27Z [Term] id: MI:1108 name: biocarta namespace: PSI-MI def: "BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways." [PMID:14760721] synonym: "biocarta" EXACT PSI-MI-short [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-07-07T03:05:55Z [Term] id: MI:1109 name: gene database namespace: PSI-MI def: "Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes." [PMID:14755292] subset: PSI-MI_slim synonym: "gene dbs" EXACT PSI-MI-short [] is_a: MI:0473 ! participant database created_by: orchard creation_date: 2011-07-08T08:00:33Z [Term] id: MI:1110 name: predicted interaction namespace: PSI-MI def: "Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method." [PMID:14755292] subset: PSI-MI_slim synonym: "predicted" EXACT PSI-MI-short [] is_a: MI:0190 ! interaction type created_by: orchard creation_date: 2011-08-03T11:14:11Z [Term] id: MI:1111 name: two hybrid bait or prey pooling approach namespace: PSI-MI def: "Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners." [PMID:11283351, PMID:20946815] subset: PSI-MI_slim is_a: MI:0398 ! two hybrid pooling approach created_by: orchard creation_date: 2011-09-29T03:19:21Z [Term] id: MI:1112 name: two hybrid prey pooling approach namespace: PSI-MI def: "Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners." [PMID:20946815] subset: PSI-MI_slim is_a: MI:1111 ! two hybrid bait or prey pooling approach created_by: orchard creation_date: 2011-09-29T03:21:01Z [Term] id: MI:1113 name: two hybrid bait and prey pooling approach namespace: PSI-MI def: "def" [PMID:10655498] subset: PSI-MI_slim is_a: MI:0398 ! two hybrid pooling approach created_by: orchard creation_date: 2011-09-29T03:23:17Z [Term] id: MI:1114 name: virhostnet namespace: PSI-MI def: "A database of viral-host interactions." [PMID:18984613] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-10-19T01:28:24Z [Term] id: MI:1115 name: spike namespace: PSI-MI def: "SPIKE" [PMID:21097778] subset: PSI-MI_slim synonym: "Signalling Pathways Integrated Knowledge Engine" EXACT [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-11-09T10:27:04Z [Term] id: MI:1116 name: genemania namespace: PSI-MI def: "GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity." [PMID:20576703] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-11-09T02:13:28Z [Term] id: MI:1117 name: topfind namespace: PSI-MI def: "TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided." [PMID:21822272] subset: PSI-MI_slim synonym: "Termini-oriented protein function inferred database" EXACT [] is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-11-16T11:09:25Z [Term] id: MI:1118 name: enhanced yellow fluorescent protein tag namespace: PSI-MI def: "A variation of yellow fluorescent protein derived from eGFP." [PMID:10929120] subset: PSI-MI_slim synonym: "eyfp" EXACT PSI-MI-short [] is_a: MI:0368 ! yellow fluorescent protein tag created_by: orchard creation_date: 2011-11-24T03:17:33Z [Term] id: MI:1119 name: nYFP namespace: PSI-MI def: "n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:11983170] subset: PSI-MI_slim synonym: "N-terminal part of YFP" RELATED [] is_a: MI:0368 ! yellow fluorescent protein tag created_by: orchard creation_date: 2011-11-24T03:30:18Z [Term] id: MI:1120 name: cYFP namespace: PSI-MI def: "c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:11983170] subset: PSI-MI_slim synonym: "C-terminal part of YFP" RELATED [] is_a: MI:0368 ! yellow fluorescent protein tag created_by: orchard creation_date: 2011-11-24T03:43:07Z [Term] id: MI:1121 name: ceYFP namespace: PSI-MI def: "c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:11983170] subset: PSI-MI_slim synonym: "C-terminal part of EYFP" RELATED [] is_a: MI:1118 ! enhanced yellow fluorescent protein tag created_by: orchard creation_date: 2011-11-24T03:43:30Z [Term] id: MI:1122 name: neYFP namespace: PSI-MI def: "n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC)." [PMID:11983170] subset: PSI-MI_slim synonym: "N-terminal part of EYFP" RELATED [] is_a: MI:1118 ! enhanced yellow fluorescent protein tag created_by: orchard creation_date: 2011-11-24T03:44:40Z [Term] id: MI:1123 name: bindingdb namespace: PSI-MI def: "A web-accessible database of experimentally determined protein-ligand binding affinities." [PMID:17145705] subset: PSI-MI_slim is_a: MI:0461 ! interaction database created_by: orchard creation_date: 2011-11-28T08:55:26Z [Term] id: MI:1124 name: pathwaycommons namespace: PSI-MI def: "Allows the user to browse and search pathways across multiple public pathway databases.\nhttp://www.pathwaycommons.org" [PMID:21071392] subset: PSI-MI_slim synonym: "Pathway Commons" EXACT [] is_a: MI:1106 ! pathways database created_by: orchard creation_date: 2011-11-30T03:04:14Z [Term] id: MI:1125 name: direct binding region namespace: PSI-MI def: "The defined region of protein which makes physical contact with the interacting partner." [PMID:14755292] comment: Should normally be used with X-ray crystallography or NMR data. subset: PSI-MI_slim synonym: "direct binding" EXACT PSI-MI-short [] is_a: MI:0442 ! sufficient binding region created_by: orchard creation_date: 2012-01-03T01:10:25Z [Term] id: MI:1126 name: self interaction namespace: PSI-MI def: "A region of a molecule which is involved in an inter-molecular interaction." [PMID:14755292] comment: The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information. subset: PSI-MI_slim is_a: MI:0407 ! direct interaction created_by: orchard creation_date: 2012-01-03T01:19:22Z [Term] id: MI:1127 name: putative self interaction namespace: PSI-MI def: "A region of a molecule which is putatively involved in an inter-molecular interaction." [PMID:14755292] comment: The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information. subset: PSI-MI_slim is_a: MI:0407 ! direct interaction created_by: orchard creation_date: 2012-01-03T01:21:58Z [Term] id: MI:1128 name: mutation disrupting interaction strength namespace: PSI-MI def: "Region of a molecule whose mutation or deletion totally disrupts an interaction strength." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation disrupting strength" EXACT PSI-MI-short [] is_a: MI:0573 ! mutation disrupting interaction created_by: orchard creation_date: 2012-01-03T01:36:37Z [Term] id: MI:1129 name: mutation disrupting interaction rate namespace: PSI-MI def: "Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction).." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation disrupting rate" EXACT PSI-MI-short [] is_a: MI:0573 ! mutation disrupting interaction created_by: orchard creation_date: 2012-01-03T01:37:43Z [Term] id: MI:1130 name: mutation decreasing interaction rate namespace: PSI-MI def: "Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction)." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation deceasing rate" EXACT PSI-MI-short [] is_a: MI:0119 ! mutation decreasing interaction created_by: orchard creation_date: 2012-01-03T01:38:58Z [Term] id: MI:1131 name: mutation increasing interaction rate namespace: PSI-MI def: "Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction)." [PMID:14577292] subset: PSI-MI_slim synonym: "mutation increasing rate" EXACT PSI-MI-short [] is_a: MI:0382 ! mutation increasing interaction created_by: orchard creation_date: 2012-01-03T01:45:09Z [Term] id: MI:1132 name: mutation increasing interaction strength namespace: PSI-MI def: "Region of a molecule whose mutation or deletion increases significantly interaction strength." [PMID:14577292] subset: PSI-MI_slim synonym: "mutation increasing strength" EXACT PSI-MI-short [] is_a: MI:0382 ! mutation increasing interaction created_by: orchard creation_date: 2012-01-03T01:45:42Z [Term] id: MI:1133 name: mutation decreasing interaction strength namespace: PSI-MI def: "Region of a molecule whose mutation or deletion decreases significantly interaction strength." [PMID:14755292] subset: PSI-MI_slim synonym: "mutation deceasing strength" EXACT PSI-MI-short [] is_a: MI:0119 ! mutation decreasing interaction created_by: orchard creation_date: 2012-01-03T01:48:40Z [Term] id: MI:1134 name: mcherry fluorescent protein tag namespace: PSI-MI def: "mCherry is a red monomer which matures extremely rapidly, making it possible to see results very soon after activating transcription. It is highly photostable and resistant to photobleaching. Excitation maximum: 587 nm. Emission maximum: 610 nm." [] synonym: "mcherry" EXACT PSI-MI-short [] is_a: MI:0732 ! red fluorescent protein tag created_by: orchard creation_date: 2012-01-03T02:53:23Z [Term] id: MI:1135 name: venus fluorescent protein tag namespace: PSI-MI def: "Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively." [PMID:14755292] subset: PSI-MI_slim synonym: "venus" EXACT PSI-MI-short [] is_a: MI:0368 ! yellow fluorescent protein tag created_by: orchard creation_date: 2012-01-03T03:05:01Z [Term] id: MI:1136 name: kusabira-green protein tag namespace: PSI-MI def: "Monomeric coral fluorescent reporter protein." [PMID:14755292] subset: PSI-MI_slim synonym: "kusabira-green" EXACT PSI-MI-short [] is_a: MI:0367 ! green fluorescent protein tag created_by: orchard creation_date: 2012-01-03T03:10:28Z [Term] id: MI:1137 name: carboxylation assay namespace: PSI-MI def: "The measurement of a the introduction of a carboxylic acid group into a substrate." [PMID:14755292] subset: PSI-MI_slim synonym: "carboxylation assay" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T03:17:56Z [Term] id: MI:1138 name: decarboxylation assay namespace: PSI-MI def: "The measurement of a the introduction of a carboxylic acid group into a substrate." [PMID:14755292] subset: PSI-MI_slim synonym: "decarboxxylation assay" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T03:22:04Z [Term] id: MI:1139 name: carboxylation reaction namespace: PSI-MI def: "Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins." [PMID:14755292] subset: PSI-MI_slim synonym: "carboxylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T03:24:05Z [Term] id: MI:1140 name: decarboxylation reaction namespace: PSI-MI def: "Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1)." [PMID:14755292] subset: PSI-MI_slim synonym: "decarboxylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T03:31:42Z [Term] id: MI:1141 name: s tag namespace: PSI-MI def: "S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0507 ! tag created_by: orchard creation_date: 2012-01-03T03:37:51Z [Term] id: MI:1142 name: aminoacylation assay namespace: PSI-MI def: "The measurement of the addition of an aminoacyl group to a compound." [PMID:14755292] subset: PSI-MI_slim synonym: "aminoacylation" EXACT PSI-MI-short [] is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T03:46:46Z [Term] id: MI:1143 name: aminoacylation reaction namespace: PSI-MI def: "Aminoacylation is the process of adding an aminoacyl group to a compound." [PMID:14755292] subset: PSI-MI_slim synonym: "aminoacylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T03:49:50Z [Term] id: MI:1144 name: protein a tag visualisation namespace: PSI-MI def: "Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A." [PMID:14755292] subset: PSI-MI_slim synonym: "protein a visualisation" EXACT PSI-MI-short [] is_a: MI:0866 ! tag visualisation created_by: orchard creation_date: 2012-01-03T03:54:35Z [Term] id: MI:1145 name: phospholipase assay namespace: PSI-MI def: "A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T04:04:16Z [Term] id: MI:1146 name: phospholipase reaction namespace: PSI-MI def: "Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T04:08:14Z [Term] id: MI:1147 name: ampylation assay namespace: PSI-MI def: "Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino\nacids." [PMID:14755292] subset: PSI-MI_slim is_a: MI:0415 ! enzymatic study created_by: orchard creation_date: 2012-01-03T04:18:27Z [Term] id: MI:1148 name: ampylation reaction namespace: PSI-MI def: "AMPylation, previously known as adenylylation, is formation of a\nphosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys\n(RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino\nacids." [PMID:14755292] subset: PSI-MI_slim synonym: "ampylation" EXACT PSI-MI-short [] is_a: MI:0414 ! enzymatic reaction created_by: orchard creation_date: 2012-01-03T04:21:12Z [Term] id: MI:2002 name: drugbank namespace: PSI-MI def: "DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins." [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2003 name: commercial name namespace: PSI-MI def: "Standard name of drug or any reagent as provided by its manufacturer." [PMID:14755292] subset: Drugable synonym: "generic name" EXACT PSI-MI-alternate [] is_a: MI:1041 ! synonym [Term] id: MI:2004 name: drug brand name namespace: PSI-MI def: "Alternate names of the drug, brand names from different manufacturers." [PMID:14755292] subset: Drugable is_a: MI:1041 ! synonym [Term] id: MI:2005 name: drug mixture brand name namespace: PSI-MI def: "Brand names and composition of mixtures that include the drug described in this DrugCard file." [PMID:14755292] subset: Drugable synonym: "mix brand name" EXACT PSI-MI-short [] is_a: MI:1041 ! synonym [Term] id: MI:2006 name: biotech product preparation namespace: PSI-MI def: "Description of the drug (for biotech drugs) describing its composition and/or preparation." [PMID:14755292] subset: Drugable synonym: "biotech prep" EXACT PSI-MI-short [] is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2007 name: iupac name namespace: PSI-MI def: "IUPAC or standard chemical name for a drug, or a chemical." [PMID:14755292] subset: Drugable is_a: MI:1041 ! synonym [Term] id: MI:2008 name: chemical formula namespace: PSI-MI def: "Chemical formula describing atomic or elemental composition" [PMID:14755292] subset: Drugable is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2009 name: chemical structure namespace: PSI-MI def: "Image of the drug structure (if small molecule) or its sequence (if biotech drug)" [PMID:14755292] subset: Drugable is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2010 name: standard inchi namespace: PSI-MI def: "IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03." [PMID:14755292] subset: PSI-MI_slim synonym: "inchi id" RELATED [] synonym: "standard inchi" EXACT PSI-MI-short [] is_a: MI:2091 ! structure representation attribute name [Term] id: MI:2011 name: cas registry number namespace: PSI-MI def: "Chemical Abstract Service identification number" [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2012 name: kegg compound namespace: PSI-MI def: "Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)" [PMID:14755292] subset: Drugable synonym: "KEGG Compound ID" EXACT PSI-MI-alternate [] is_a: MI:0470 ! kegg [Term] id: MI:2013 name: pubchem namespace: PSI-MI def: "NCBI's PubChem database identification number (if molecule is in PubChem).\nOBSOLETE as redudant with MI:0730" [PMID:14755292] subset: Drugable synonym: "PubChem ID" EXACT PSI-MI-alternate [] is_obsolete: true [Term] id: MI:2015 name: pharmgkb namespace: PSI-MI def: "Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)" [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2016 name: bind smid namespace: PSI-MI def: "BIND database Small Molecule Identification number (if molecule is in BIND)" [PMID:14755292] comment: May not be publicly available any more since now owned by Thompson Scientific. subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2017 name: heterogen namespace: PSI-MI def: "The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for\nwhich coordinates are supplied. Groups are considered HET if they are: \n- not one of the standard amino acids, and \n- not one of the nucleic acids (C, G, A, T, U, and I), and \n- not one of the modified versions of nucleic acids (+C, +G, +A,\n+T, +U, and +I), and \n- not an unknown amino acid or nucleic acid where UNK is used to\nindicate the unknown residue name. \nHet records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK." [PMID:14755292] subset: Drugable synonym: "het" EXACT PSI-MI-short [] is_a: MI:0460 ! rcsb pdb is_a: MI:0472 ! pdbe is_a: MI:0806 ! pdbj [Term] id: MI:2020 name: canadian drug identification number namespace: PSI-MI def: "Drug Identification Number (Canadian Drug ID system)" [PMID:14755292] subset: Drugable synonym: "din" EXACT PSI-MI-short [] is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2021 name: rxlist link namespace: PSI-MI def: "Hyperlink to RxList entry for the given drug (if it exists)" [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2023 name: material safety data sheet namespace: PSI-MI def: "Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs." [PMID:14755292] subset: Drugable synonym: "msds" EXACT PSI-MI-short [] synonym: "MSDS Material Safety Sheet" EXACT PSI-MI-alternate [] is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2024 name: patent number namespace: PSI-MI def: "number of the patent describing a drug's synthesis or use." [PMID:14755292] subset: Drugable is_a: MI:0353 ! cross-reference type [Term] id: MI:2025 name: molecular weight namespace: PSI-MI def: "Molecular weight in g/mol, determined from molecular formula or sequence." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2026 name: melting point namespace: PSI-MI def: "The melting point of a solid is the temperature range at which it changes state from solid to liquid." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2027 name: water solubility namespace: PSI-MI def: "Water solubility in mg/mL or g/L" [PMID:14755292] subset: Drugable synonym: "logSw" EXACT PSI-MI-alternate [] is_a: MI:2160 ! logs [Term] id: MI:2029 name: logp namespace: PSI-MI def: "Water/octanol partition coefficient of a small molecule." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2030 name: isoelectric point namespace: PSI-MI def: "The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2033 name: hydrophobicity namespace: PSI-MI def: "Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2036 name: boiling point namespace: PSI-MI def: "The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2039 name: smiles string namespace: PSI-MI def: "SMILES string corresponding to drug structure" [PMID:14755292] subset: Drugable is_a: MI:2091 ! structure representation attribute name [Term] id: MI:2040 name: drug type namespace: PSI-MI def: "Type of drug (approved, experimental, biotech, nutraceutical)" [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2041 name: drug category namespace: PSI-MI def: "Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.)." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2042 name: disease indication namespace: PSI-MI def: "Description or common names of diseases that the drug is used to treat." [PMID:14755292] comment: Source of further terms could be MeSH term or SNOWMAN. subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2043 name: pharmacology namespace: PSI-MI def: "Text description of how the drug works at a clinical or physiological level." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2044 name: mechanism of action namespace: PSI-MI def: "Description of how the drug works or what it binds to at a molecular level." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2045 name: drug absorption namespace: PSI-MI def: "Determination of how quickly and how much of a drug reaches its intended target (site) of action." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2046 name: lethal dose 50 namespace: PSI-MI def: "The LD50 is the dose that kills half (50%) of the animals tested" [PMID:14755292] subset: Drugable synonym: "ld50" EXACT PSI-MI-alternate [] synonym: "lethal dose 50 %" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2047 name: percentage of plasma protein binding namespace: PSI-MI def: "Percentage of the drug that is bound in plasma proteins" [PMID:14755292] subset: Drugable synonym: "plasma prot binding" EXACT PSI-MI-short [] synonym: "protein binding %" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2048 name: drug biotransformation namespace: PSI-MI def: "The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media." [PMID:14755292] subset: Drugable synonym: "drug metabolism" EXACT PSI-MI-short [] is_a: MI:2115 ! pharmacokinetics attribute name [Term] id: MI:2049 name: elimination half life namespace: PSI-MI def: "Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%." [PMID:14755292] subset: Drugable synonym: "distribution halflife" EXACT PSI-MI-alternate [] synonym: "elimin half life" EXACT PSI-MI-short [] synonym: "t1/2" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2050 name: dosage form namespace: PSI-MI def: "How the drug is dispensed (tablets, capsules, solutions), packing material." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2051 name: patient information namespace: PSI-MI def: "Information on the disease indications and treatment regime for the drug. May also include contra-indications." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2053 name: contraindications namespace: PSI-MI def: "Cautions or conditions indicating why or when the drug should not be taken or prescribed." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2054 name: bioactive entity reference namespace: PSI-MI def: "General on-line reference to other details about a drug or other bioactive entity." [PMID:14755292] subset: Drugable subset: PSI-MI_slim synonym: "bioactive entity ref" EXACT PSI-MI-short [] is_a: MI:0473 ! participant database [Term] id: MI:2055 name: chemical stability namespace: PSI-MI def: "chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent." [PMID:14755292] subset: Drugable synonym: "thermodynamic stability" EXACT PSI-MI-alternate [] is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2064 name: solubility namespace: PSI-MI def: "Potential ability of a substance to dissolve in a liquid." [PMID:14755292] subset: Drugable synonym: "dt theoretical pi" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2084 name: organisms affected namespace: PSI-MI def: "Names of organisms which are affected, positively or negatively, by the drug." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2086 name: physicochemical attribute name namespace: PSI-MI def: "Chemical and physical properties of a molecule." [PMID:14755292] subset: Drugable synonym: "physicochemical att" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:2089 name: bioactive entity attribute name namespace: PSI-MI def: "Properties of a chemical tested or used as a drug, herbicide, insecticide etc." [PMID:14755292] subset: Drugable synonym: "bioactive entity att" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:2091 name: structure representation attribute name namespace: PSI-MI def: "Human artefact to describe and report the structure of a molecule." [PMID:14755292] subset: Drugable synonym: "struc representation" EXACT PSI-MI-short [] is_a: MI:0590 ! attribute name [Term] id: MI:2097 name: anti-convulsant namespace: PSI-MI def: "Therapeutic category or general category of drug -anti-convulsant" [PMID:14755292] subset: Drugable is_a: MI:2041 ! drug category [Term] id: MI:2098 name: anti-bacterial namespace: PSI-MI def: "Therapeutic category or general category of drug -anti-bacterial" [PMID:14755292] subset: Drugable is_a: MI:2041 ! drug category [Term] id: MI:2099 name: fda approved drug namespace: PSI-MI def: "A drug licensed for sale in the USA by the FDA." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2100 name: experimental drug namespace: PSI-MI def: "A drug which has yet to be formally approved for the indication which it is currently being used to treat." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2101 name: biotech drug namespace: PSI-MI def: "A natural product, such as a protein or peptide, which is produced used biotechnology as a drug." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2102 name: nutraceutical drug namespace: PSI-MI def: "A drug which may also be regarded as a foodstuff." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2105 name: pka namespace: PSI-MI def: "Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2106 name: degree of ionisation ph 7.4 namespace: PSI-MI def: "The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "ionisation ph 7.4" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2107 name: logd namespace: PSI-MI def: "The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2108 name: solubility ph 7.4 namespace: PSI-MI def: "Solubility pH 7.4" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:2064 ! solubility [Term] id: MI:2109 name: solubility in dmso namespace: PSI-MI def: "Solubility in DMSO" [PMID:14755292] subset: Drugable is_a: MI:2064 ! solubility [Term] id: MI:2111 name: diffusion coefficient namespace: PSI-MI def: "Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "diffusion coeff" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2112 name: chemical stability at pH 2 namespace: PSI-MI def: "Chemical stability at pH 2" [PMID:14755292] comment: Qualitative prediction of this parameter is possible. subset: Drugable synonym: "chem stab ph 2" EXACT PSI-MI-short [] is_a: MI:2055 ! chemical stability [Term] id: MI:2113 name: dissolution profile namespace: PSI-MI def: "The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations." [PMID:14755292] comment: The prediction of the value for this paramter is currently not possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2115 name: pharmacokinetics attribute name namespace: PSI-MI def: "Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug." [PMID:14755292] subset: Drugable is_a: MI:2086 ! physicochemical attribute name [Term] id: MI:2116 name: cell permeability namespace: PSI-MI def: "The permitting or activating of the passage of substances into, out of, or through cells." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2118 name: volume of distribution namespace: PSI-MI def: "The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "distribution volume" EXACT PSI-MI-alternate [] synonym: "vd" EXACT PSI-MI-alternate [] synonym: "vol of distribution" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2120 name: tissue distribution namespace: PSI-MI def: "Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2121 name: transporter binding namespace: PSI-MI def: "Substrate of a carrier system allowing the intake of an agent into an organ or part of body." [PMID:14755292] comment: The prediction of the value for this parameter is currently not possible. subset: Drugable is_a: MI:2115 ! pharmacokinetics attribute name [Term] id: MI:2122 name: clearance namespace: PSI-MI def: "The ratio of excretion is or measure of the speed at which a constituent is lost from the body." [PMID:14755292] subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2123 name: renal clearance namespace: PSI-MI def: "The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2124 name: total clearance namespace: PSI-MI def: "The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood." [PMID:14755292] comment: The prediction of the value for this paramter is currently not possible. subset: Drugable synonym: "cl" EXACT PSI-MI-alternate [] synonym: "clearance" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2125 name: maximum absorbable dose namespace: PSI-MI def: "The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier." [PMID:8987073] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "mad" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2126 name: paracellular absorption namespace: PSI-MI def: "Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "paracellular absorp" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2127 name: tmax/cmax namespace: PSI-MI def: "Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself." [PMID:14755292] comment: The prediction of the value for this paramter is currently not possible. subset: Drugable is_a: MI:0640 ! parameter type [Term] id: MI:2128 name: ABCB1 transporter substrate namespace: PSI-MI def: "Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable synonym: "abcb1 substrate" EXACT PSI-MI-short [] synonym: "pgp(mdr1) substrate " EXACT PSI-MI-alternate [] is_a: MI:2121 ! transporter binding [Term] id: MI:2129 name: bile transporter substrate namespace: PSI-MI def: "Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." [PMID:14755292] comment: The prediction of the value for this paramater is currently not possible. subset: Drugable synonym: "bile trans substrate" EXACT PSI-MI-short [] is_a: MI:2121 ! transporter binding [Term] id: MI:2130 name: cyp-450 inhibition namespace: PSI-MI def: "Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable synonym: "cyp-450 inhibition" EXACT PSI-MI-alternate [] synonym: "Cytochrome P450 inhibition" EXACT PSI-MI-alternate [] is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2131 name: metabolite identification namespace: PSI-MI def: "Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body" [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable synonym: "metabolite identific" EXACT PSI-MI-short [] is_a: MI:2115 ! pharmacokinetics attribute name [Term] id: MI:2132 name: gsh adducts namespace: PSI-MI def: "Derivative molecule which has formed from a reaction with glutathione." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2115 ! pharmacokinetics attribute name [Term] id: MI:2133 name: neutralization by glucuronidation or sulfatation namespace: PSI-MI def: "Neutralization of a compound occuring via its glucuronidation or sulfatation." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "neutraliz gluc/sulf" EXACT PSI-MI-short [] is_a: MI:2048 ! drug biotransformation [Term] id: MI:2135 name: toxicity attribute name namespace: PSI-MI def: "The mechanism by which a substance can harm humans or animals." [PMID:14755292] subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2136 name: herg binding namespace: PSI-MI def: "Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2137 name: genotoxicity namespace: PSI-MI def: "Tendency of a bioactive entity to induce damage at the level of the gene." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2138 name: mutagenicity namespace: PSI-MI def: "Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2139 name: carcinogenicity namespace: PSI-MI def: "Tendency of a bioactive entity to induce a cancer." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable synonym: "cancerogenicity" EXACT PSI-MI-alternate [] is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2140 name: chromosome damage namespace: PSI-MI def: "Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2141 name: hepatotoxicity namespace: PSI-MI def: "Tendency of a bioactive entity to affect liver function." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2142 name: phospholipidosis namespace: PSI-MI def: "Causes excess phospholipids to accumulate within cells." [PMID:14755292] comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown. subset: Drugable is_a: MI:2135 ! toxicity attribute name [Term] id: MI:2145 name: solubility ph 6.5 namespace: PSI-MI def: "Solubility pH 6.5." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable is_a: MI:2064 ! solubility [Term] id: MI:2146 name: solubility ph 2.0 namespace: PSI-MI def: "Solubility pH 2.0" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "solubility ph2.0" EXACT PSI-MI-alternate [] is_a: MI:2064 ! solubility [Term] id: MI:2147 name: chemical stability at pH 7.4 namespace: PSI-MI def: "Chemical stabilityat at pH 7.4" [PMID:14755292] comment: Qualitative prediction of this parameter is possible. subset: Drugable synonym: "chem stab ph 7.4" EXACT PSI-MI-short [] is_a: MI:2055 ! chemical stability [Term] id: MI:2148 name: investigational drug namespace: PSI-MI def: "A drug currently under clinical development." [PMID:14755292] comment: Intact. subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2149 name: withdrawn drug namespace: PSI-MI def: "A drug for which the licencing for prescriptive use has been withdrawn." [PMID:14755292] comment: Intact. subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2150 name: illicit drug namespace: PSI-MI def: "A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription." [PMID:14755292] subset: Drugable is_a: MI:2040 ! drug type [Term] id: MI:2151 name: other drug interaction namespace: PSI-MI def: "Effect of additional drug treatments on a given drug action." [PMID:14755292] subset: Drugable synonym: "drug interaction" EXACT PSI-MI-short [] is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2152 name: food interaction namespace: PSI-MI def: "Effect of food ingestion on a given drug treatment." [PMID:14755292] comment: IntAct MeSH term or SNOWMAN. subset: Drugable is_a: MI:2089 ! bioactive entity attribute name [Term] id: MI:2153 name: pdr health namespace: PSI-MI def: "Hyperlink to PDRhealth entry for the given drug (if it exists)" [PMID:14755292] subset: Drugable synonym: "PDRhealth" EXACT PSI-MI-alternate [] is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2154 name: wikipedia namespace: PSI-MI def: "Hyperlink to wikipedia entry for the given drug (if it exists)" [PMID:14755292] subset: Drugable is_a: MI:2054 ! bioactive entity reference [Term] id: MI:2155 name: average molecular weight namespace: PSI-MI def: "Molecular weight in g/mol, determined from molecular formula or sequence." [PMID:14755292] subset: Drugable synonym: "avrg mol weight" EXACT PSI-MI-short [] is_a: MI:2025 ! molecular weight [Term] id: MI:2156 name: monoisotopic molecular weight namespace: PSI-MI def: "Molecular weight in g/mol, determined from molecular formula or sequence." [PMID:14755292] subset: Drugable synonym: "monoisotopic mol wgt" EXACT PSI-MI-short [] is_a: MI:2025 ! molecular weight [Term] id: MI:2157 name: experimental water solubility namespace: PSI-MI def: "Water solubility in mg/mL or g/L." [PMID:14755292] subset: Drugable synonym: "exp h2o solubilty" EXACT PSI-MI-short [] synonym: "experimental h2o solubility" EXACT PSI-MI-alternate [] is_a: MI:2027 ! water solubility is_a: MI:2161 ! experimental logs [Term] id: MI:2158 name: predicted water solubility namespace: PSI-MI def: "Water solubility in mg/mL or g/L" [PMID:14755292] subset: Drugable synonym: "predicted h2o solub" EXACT PSI-MI-short [] synonym: "predicted h2o solubility" EXACT PSI-MI-alternate [] is_a: MI:2027 ! water solubility [Term] id: MI:2160 name: logs namespace: PSI-MI def: "Solubility of a molecule in a given solvant." [PMID:14755292] subset: Drugable synonym: "logS" EXACT PSI-MI-alternate [] is_a: MI:0640 ! parameter type [Term] id: MI:2161 name: experimental logs namespace: PSI-MI def: "Experimental derived value for the solubility of a molecule in a given solvant." [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "experimental logS" EXACT PSI-MI-alternate [] is_a: MI:2160 ! logs [Term] id: MI:2162 name: experimental CaCO2 permeability namespace: PSI-MI def: "Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption" [PMID:14755292] comment: Quantitative prediction of this parameter is possible. subset: Drugable synonym: "caco2 permeability" EXACT PSI-MI-short [] is_a: MI:0640 ! parameter type [Term] id: MI:2163 name: by homology namespace: PSI-MI def: "Reference assigned to a molecule by sequence homology with another similar sequence." [PMID:14755292] subset: Drugable is_a: MI:0353 ! cross-reference type [Term] id: MOD:00000 name: protein modification namespace: PSI-MOD def: "Covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModRes" EXACT PSI-MOD-short [] is_a: MI:0252 ! biological feature [Term] id: MOD:00001 name: alkylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with an alkyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "AlkylRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00002 name: O-glycosyl-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O3-glycosylserine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OGlycoSer" EXACT PSI-MOD-short [] xref: DiffAvg: "146.14" xref: DiffFormula: "C 6 H 10 N 0 O 4" xref: DiffMono: "146.057909" xref: Formula: "C 9 H 15 N 1 O 6" xref: MassAvg: "233.22" xref: MassMono: "233.089937" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00396 ! O-glycosylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00005 name: O-glycosyl-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to O3-glycosylthreonine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OGlycoThr" EXACT PSI-MOD-short [] xref: DiffAvg: "146.14" xref: DiffFormula: "C 6 H 10 N 0 O 4" xref: DiffMono: "146.057909" xref: Formula: "C 10 H 17 N 1 O 6" xref: MassAvg: "247.25" xref: MassMono: "247.105587" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00396 ! O-glycosylated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00006 name: N-glycosylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydrogen atom on a nitrogen with a carbohydrate-like group through a glycosidic bond." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NGlycoRes" EXACT PSI-MOD-short [] is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00009 name: natural residue namespace: PSI-MOD def: "A protein modification that inserts or replaces a residue with a natural, standard or nonstandard, encoded residue." [PubMed:18688235, PubMed:6692818] subset: PSI-MOD_slim synonym: "Res" EXACT PSI-MOD-short [] xref: Origin: "X" xref: Source: "natural" is_a: MOD:01157 ! protein modification categorized by amino acid modified [Term] id: MOD:00010 name: L-alanine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-alanine." [ChEBI:29948, DeltaMass:0, PubMed:6692818, RESID:AA0001] subset: PSI-MOD_slim synonym: "(S)-2-aminopropanoic acid" EXACT RESID-systematic [] synonym: "2-aminopropionic acid" EXACT RESID-alternate [] synonym: "Ala" EXACT PSI-MOD-short [] synonym: "alpha-alanine" EXACT RESID-alternate [] synonym: "alpha-aminopropionic acid" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 3 H 5 N 1 O 1" xref: MassAvg: "71.08" xref: MassMono: "71.037114" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00011 name: L-arginine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-arginine." [ChEBI:29952, DeltaMass:0, PubMed:518876, PubMed:6692818, RESID:AA0002] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-(carbamimidamido)pentanoic acid" EXACT RESID-systematic [] synonym: "2-amino-5-[(aminoiminomethyl)amino]pentanoic acid" EXACT RESID-alternate [] synonym: "2-amino-5-guanidinopentanoic acid" EXACT RESID-alternate [] synonym: "2-amino-5-guanidinovaleric acid" EXACT RESID-alternate [] synonym: "alpha-amino-delta-guanidinovaleric acid" EXACT RESID-alternate [] synonym: "Arg" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 6 H 12 N 4 O 1" xref: MassAvg: "156.19" xref: MassMono: "156.101111" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00012 name: L-asparagine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-asparagine." [ChEBI:29956, DeltaMass:0, PubMed:15736973, PubMed:5681232, PubMed:6692818, PubMed:9789001, RESID:AA0003] subset: PSI-MOD_slim synonym: "(S)-2-amino-4-butanediamic acid" EXACT RESID-systematic [] synonym: "2,4-diamino-4-oxobutanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-carbamoylpropanoic acid" EXACT RESID-alternate [] synonym: "2-aminosuccinamic acid" EXACT RESID-alternate [] synonym: "alpha-amino-beta-carbamylpropionic acid" EXACT RESID-alternate [] synonym: "alpha-aminosuccinamic acid" EXACT RESID-alternate [] synonym: "Asn" EXACT PSI-MOD-short [] synonym: "aspartic acid beta-amide" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 4 H 6 N 2 O 2" xref: MassAvg: "114.10" xref: MassMono: "114.042927" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00013 name: L-aspartic acid residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-aspartic acid." [ChEBI:29958, DeltaMass:0, PubMed:1097438, PubMed:339692, PubMed:4399050, PubMed:5764436, PubMed:6692818, PubMed:8089117, PubMed:9521123, PubMed:9582379, RESID:AA0004] subset: PSI-MOD_slim synonym: "(S)-2-aminobutanedioic acid" EXACT RESID-systematic [] synonym: "aminosuccinic acid" EXACT RESID-alternate [] synonym: "Asp" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 4 H 5 N 1 O 3" xref: MassAvg: "115.09" xref: MassMono: "115.026943" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00014 name: L-cysteine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-cysteine." [ChEBI:29950, DeltaMass:0, PubMed:1310545, PubMed:15790858, PubMed:3447159, PubMed:6692818, PubMed:7338899, RESID:AA0005] comment: From DeltaMass: Average Mass: 121. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "(R)-cysteine" EXACT RESID-alternate [] synonym: "2-amino-3-mercaptopropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-mercaptopropionic acid" EXACT RESID-alternate [] synonym: "3-mercapto-L-alanine" EXACT RESID-alternate [] synonym: "alpha-amino-beta-mercaptopropanoic acid" EXACT RESID-alternate [] synonym: "alpha-amino-beta-mercaptopropionic acid" EXACT RESID-alternate [] synonym: "alpha-amino-beta-thiolpropionic acid" EXACT RESID-alternate [] synonym: "beta-mercaptoalanine" EXACT RESID-alternate [] synonym: "Cys" EXACT PSI-MOD-short [] synonym: "Cysteine (C, Cys)" EXACT DeltaMass-label [] synonym: "half-cystine" EXACT RESID-alternate [] synonym: "L-(+)-cysteine" EXACT RESID-alternate [] synonym: "thioserine" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0 S 0" xref: DiffMono: "0.000000" xref: Formula: "C 3 H 5 N 1 O 1 S 1" xref: MassAvg: "103.14" xref: MassMono: "103.009185" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00015 name: L-glutamic acid residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-glutamic acid." [ChEBI:29972, DeltaMass:0, PubMed:1881881, PubMed:4565668, PubMed:4922541, PubMed:6692818, PubMed:9326660, PubMed:957425, RESID:AA0006] subset: PSI-MOD_slim synonym: "(S)-2-aminopentanedioic acid" EXACT RESID-systematic [] synonym: "1-aminopropane-1,3-dicarboxylic acid" EXACT RESID-alternate [] synonym: "alpha-aminoglutaric acid" EXACT RESID-alternate [] synonym: "Glu" EXACT PSI-MOD-short [] synonym: "glutaminic acid" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 5 H 7 N 1 O 3" xref: MassAvg: "129.11" xref: MassMono: "129.042593" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00016 name: L-glutamine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-glutamine." [ChEBI:30011, DeltaMass:0, PubMed:3340166, PubMed:6692818, PubMed:9342308, RESID:AA0007] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-pentanediamic acid" EXACT RESID-systematic [] synonym: "2,5-diamino-5-oxopentanoic acid" EXACT RESID-alternate [] synonym: "2-amino-4-carbamoylbutanoic acid" EXACT RESID-alternate [] synonym: "2-aminoglutaramic acid" EXACT RESID-alternate [] synonym: "alpha-amino-gamma-carbamylbutyric acid" EXACT RESID-alternate [] synonym: "Gln" EXACT PSI-MOD-short [] synonym: "glutamic acid 5-amide" EXACT RESID-alternate [] synonym: "glutamic acid gamma-amide" EXACT RESID-alternate [] synonym: "glutamide" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 5 H 8 N 2 O 2" xref: MassAvg: "128.13" xref: MassMono: "128.058578" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00017 name: glycine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to a glycine." [ChEBI:29947, DeltaMass:0, PubMed:1310545, PubMed:6692818, RESID:AA0008] subset: PSI-MOD_slim synonym: "aminoacetic acid" EXACT RESID-alternate [] synonym: "aminoethanoic acid" EXACT RESID-systematic [] synonym: "Gly" EXACT PSI-MOD-short [] synonym: "glycocoll" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 2 H 3 N 1 O 1" xref: MassAvg: "57.05" xref: MassMono: "57.021464" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00018 name: L-histidine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-histidine." [ChEBI:29979, DeltaMass:0, PubMed:14342316, PubMed:2722967, PubMed:512, PubMed:5460889, PubMed:6129252, PubMed:6692818, PubMed:6876174, RESID:AA0009] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1H-imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "4-(2-amino-2-carboxyethyl)imidazole" EXACT RESID-alternate [] synonym: "alpha-amino-beta-(4-imidazole)propionic acid" EXACT RESID-alternate [] synonym: "His" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 6 H 7 N 3 O 1" xref: MassAvg: "137.14" xref: MassMono: "137.058912" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00019 name: L-isoleucine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-isoleucine." [ChEBI:30009, DeltaMass:0, PubMed:6692818, RESID:AA0010] subset: PSI-MOD_slim synonym: "(2S,3S)-2-amino-3-methylpentanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-methylvaleric acid" EXACT RESID-alternate [] synonym: "Ile" EXACT PSI-MOD-short [] synonym: "Isoleucyl" EXACT DeltaMass-label [] synonym: "L-threo-isoleucine" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 6 H 11 N 1 O 1" xref: MassAvg: "113.16" xref: MassMono: "113.084064" xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00020 name: L-leucine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-leucine." [ChEBI:30006, DeltaMass:0, PubMed:11478885, PubMed:6692818, RESID:AA0011] subset: PSI-MOD_slim synonym: "(S)-2-amino-4-methylpentanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-gamma-methylvaleric acid" EXACT RESID-alternate [] synonym: "alpha-aminoisocaproic acid" EXACT RESID-alternate [] synonym: "Leu" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 6 H 11 N 1 O 1" xref: MassAvg: "113.16" xref: MassMono: "113.084064" xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00021 name: L-lysine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-lysine." [ChEBI:29967, DeltaMass:0, PubMed:3106962, PubMed:6120171, PubMed:6692818, RESID:AA0012] subset: PSI-MOD_slim synonym: "(S)-2,6-diaminohexanoic acid" EXACT RESID-systematic [] synonym: "alpha,epsilon-diaminocaproic acid" EXACT RESID-alternate [] synonym: "Lys" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 6 H 12 N 2 O 1" xref: MassAvg: "128.17" xref: MassMono: "128.094963" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00022 name: L-methionine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-methionine." [ChEBI:29983, DeltaMass:0, PubMed:6411710, PubMed:6692818, RESID:AA0013] comment: From DeltaMass: Average Mass: 149 subset: PSI-MOD_slim synonym: "(S)-2-amino-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-amino-4-(methylthio)butanoic acid" EXACT RESID-alternate [] synonym: "2-amino-4-(methylthio)butyric acid" EXACT RESID-alternate [] synonym: "alpha-amino-gamma-methylmercaptobutyric acid" EXACT RESID-alternate [] synonym: "alpha-amino-gamma-methylthiobutyric acid" EXACT RESID-alternate [] synonym: "gamma-methylthio-alpha-aminobutyric acid" EXACT RESID-alternate [] synonym: "L-(-)-methionine" EXACT RESID-alternate [] synonym: "Met" EXACT PSI-MOD-short [] synonym: "S-methyl-L-homocysteine" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0 S 0" xref: DiffMono: "0.000000" xref: Formula: "C 5 H 9 N 1 O 1 S 1" xref: MassAvg: "131.20" xref: MassMono: "131.040485" xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00023 name: L-phenylalanine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-phenylalanine." [ChEBI:29997, DeltaMass:0, PubMed:6692818, RESID:AA0014] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-phenylpropanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-phenylpropionic acid" EXACT RESID-alternate [] synonym: "Phe" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 9 H 9 N 1 O 1" xref: MassAvg: "147.17" xref: MassMono: "147.068414" xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00024 name: L-proline residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-proline." [ChEBI:30017, DeltaMass:0, PubMed:6692818, PubMed:8547259, RESID:AA0015] subset: PSI-MOD_slim synonym: "(S)-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] synonym: "Pro" EXACT PSI-MOD-short [] synonym: "pyrrolidine-2-carboxylic acid" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 5 H 7 N 1 O 1" xref: MassAvg: "97.12" xref: MassMono: "97.052764" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00025 name: L-serine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-serine." [ChEBI:29999, DeltaMass:0, PubMed:4399050, PubMed:6692818, RESID:AA0016] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-hydroxypropanoic acid" EXACT RESID-systematic [] synonym: "3-hydroxy-L-alanine" EXACT RESID-alternate [] synonym: "alpha-amino-beta-hydroxypropionic acid" EXACT RESID-alternate [] synonym: "beta-hydroxyalanine" EXACT RESID-alternate [] synonym: "Ser" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 3 H 5 N 1 O 2" xref: MassAvg: "87.08" xref: MassMono: "87.032028" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00026 name: L-threonine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-threonine." [ChEBI:30013, DeltaMass:0, PubMed:2989287, PubMed:6692818, RESID:AA0017] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-hydroxybutanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-hydroxybutyric acid" EXACT RESID-alternate [] synonym: "beta-methylserine" EXACT RESID-alternate [] synonym: "L-threo-threonine" EXACT RESID-alternate [] synonym: "Thr" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 4 H 7 N 1 O 2" xref: MassAvg: "101.10" xref: MassMono: "101.047678" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00027 name: L-tryptophan residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-tryptophan." [ChEBI:29954, DeltaMass:0, PubMed:2059637, PubMed:6692818, PubMed:9324768, RESID:AA0018] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-(3-indolyl)propionoic acid" EXACT RESID-alternate [] synonym: "beta-3-indolylalanine" EXACT RESID-alternate [] synonym: "Trp" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 11 H 10 N 2 O 1" xref: MassAvg: "186.21" xref: MassMono: "186.079313" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00028 name: L-tyrosine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-tyrosine." [ChEBI:29975, DeltaMass:0, PubMed:2190093, PubMed:2542938, PubMed:5550972, PubMed:6061414, PubMed:6120171, PubMed:6692818, RESID:AA0019] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(4-hydoxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-(para-hydroxyphenyl)propionic acid" EXACT RESID-alternate [] synonym: "p-tyrosine" EXACT RESID-alternate [] synonym: "para-hydroxyphenylalanine" EXACT RESID-alternate [] synonym: "Tyr" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 9 H 9 N 1 O 2" xref: MassAvg: "163.17" xref: MassMono: "163.063329" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00029 name: L-valine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-valine." [ChEBI:30015, DeltaMass:0, PubMed:6692818, RESID:AA0020] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-methylbutanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-methylbutyric acid" EXACT RESID-alternate [] synonym: "alpha-aminoisovaleric acid" EXACT RESID-alternate [] synonym: "Val" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 5 H 9 N 1 O 1" xref: MassAvg: "99.13" xref: MassMono: "99.068414" xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01441 ! natural, standard, encoded residue [Term] id: MOD:00030 name: N-formyl-L-methionine namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an N-formyl-L-methionine, a natural pretranslational modification." [ChEBI:33718, PubMed:10825024, PubMed:11152118, PubMed:2165784, PubMed:3042771, PubMed:8758896, RESID:AA0021, UniMod:107] subset: PSI-MOD_slim synonym: "(S)-2-formylamino-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-formamido-4-(methylsulfanyl)butanoic acid" EXACT RESID-alternate [] synonym: "2-formylamino-4-(methylthio)butanoic acid" EXACT RESID-alternate [] synonym: "Addition of N-formyl met" RELATED UniMod-description [] synonym: "fMet" EXACT PSI-MOD-short [] synonym: "FormylMet" RELATED PSI-MS-label [] synonym: "N-formylated L-methionine" EXACT PSI-MOD-alternate [] synonym: "N-formylmethionine" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0 S 0" xref: DiffMono: "0.000000" xref: Formula: "C 6 H 10 N 1 O 2 S 1" xref: MassAvg: "160.21" xref: MassMono: "160.043225" xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00409 ! N-formylated residue is_a: MOD:00868 ! natural, non-standard encoded residue [Term] id: MOD:00031 name: L-selenocysteine residue namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to an L-selenocysteine, a natural pretranslational modification." [ChEBI:30000, PubMed:10523135, PubMed:1066676, PubMed:2037562, PubMed:2963330, PubMed:4734725, PubMed:6076213, PubMed:6217842, PubMed:6714945, RESID:AA0022] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-selanylpropanoic acid" EXACT RESID-systematic [] synonym: "3-selenylalanine" EXACT RESID-alternate [] synonym: "Sec" EXACT PSI-MOD-short [] synonym: "SeCys" EXACT RESID-alternate [] synonym: "selenium cysteine" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0 Se 0" xref: DiffMono: "0.000000" xref: Formula: "C 3 H 5 N 1 O 1 Se 1" xref: MassAvg: "150.04" xref: MassMono: "150.953635" xref: Origin: "U" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00745 ! selenium containing residue is_a: MOD:00859 ! modified residue that can arise from different natural residues is_a: MOD:00868 ! natural, non-standard encoded residue [Term] id: MOD:00033 name: crosslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two or more amino acid residues with covalent bonds." [PubMed:18688235] comment: The covalent bond is formed directly between sidechain atoms. If non-aminoacid atoms are involved in connecting two or more peptide chain residues peptide chain, the connection is classified as a multivalent binding site. subset: PSI-MOD_slim is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00034 name: L-cystine (cross-link) namespace: PSI-MOD def: "A protein modification that effectively cross-links two L-cysteine residues to form L-cystine." [ChEBI:16283, DeltaMass:0, PubMed:1988019, PubMed:2001356, PubMed:2076469, PubMed:3083866, PubMed:366603, PubMed:7918467, PubMed:8344916, RESID:AA0025] comment: Cross-link 2; for formation of a disulfide bond between a peptide cysteine and a free cysteine, see MOD:00765. subset: PSI-MOD_slim synonym: "(R,R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)" EXACT RESID-systematic [] synonym: "2-amino-3-(2-amino-2-carboxy-ethyl)disulfanyl-propanoic acid [misnomer]" RELATED RESID-misnomer [] synonym: "3,3'-dithiobis(2-aminopropanoic acid)" EXACT RESID-alternate [] synonym: "3,3'-dithiobisalanine" EXACT RESID-alternate [] synonym: "3,3'-dithiodialanine" EXACT RESID-alternate [] synonym: "beta,beta'-diamino-beta,beta'-dicarboxydiethyldisulfide" EXACT RESID-alternate [] synonym: "beta,beta'-dithiodialanine" EXACT RESID-alternate [] synonym: "bis(alpha-aminopropionic acid)-beta-disulfide" EXACT RESID-alternate [] synonym: "bis(beta-amino-beta-carboxyethyl)disulfide" EXACT RESID-alternate [] synonym: "Cys2" EXACT PSI-MOD-short [] synonym: "Cysteine (covalent)" EXACT UniProt-feature [] synonym: "Cystine ((Cys)2)" EXACT DeltaMass-label [] synonym: "dicysteine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 6 H 8 N 2 O 2 S 2" xref: MassAvg: "204.27" xref: MassMono: "204.002720" xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00689 ! disulfide crosslinked residues [Term] id: MOD:00035 name: (2S,3R)-3-hydroxyasparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to (2S,3R)-3-hydroxyasparagine." [PubMed:11823643, PubMed:2820791, RESID:AA0026] subset: PSI-MOD_slim synonym: "(2S,3R)-2,4-diamino-3-hydroxy-4-oxobutanoic acid" EXACT RESID-alternate [] synonym: "(2S,3R)-2-amino-3-hydroxy-4-butanediamic acid" EXACT RESID-systematic [] synonym: "(3R)-3-hydroxyasparagine" EXACT UniProt-feature [] synonym: "(3R)3HyAsn" EXACT PSI-MOD-short [] synonym: "erythro-beta-hydroxylated L-asparagine" EXACT PSI-MOD-alternate [] synonym: "L-erythro-beta-hydroxyasparagine" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 4 H 6 N 2 O 3" xref: MassAvg: "130.10" xref: MassMono: "130.037842" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00036 name: (2S,3R)-3-hydroxyaspartic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to (2S,3R)-3-hydroxyaspartic acid." [PubMed:6572939, PubMed:6871167, PubMed:8355279, RESID:AA0027] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-hydroxybutanedioic acid" EXACT RESID-systematic [] synonym: "(3R)3HyAsp" EXACT PSI-MOD-short [] synonym: "2-amino-3-hydroxysuccinic acid" EXACT RESID-alternate [] synonym: "3-hydroxyaspartate" EXACT UniProt-feature [] synonym: "3-hydroxyaspartic acid" EXACT RESID-alternate [] synonym: "erythro-beta-hydroxylated L-aspartic acid" EXACT PSI-MOD-alternate [] synonym: "L-erythro-beta-hydroxyaspartic acid" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 4 H 5 N 1 O 4" xref: MassAvg: "131.09" xref: MassMono: "131.021858" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00037 name: 5-hydroxy-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to 5-hydroxy-L-lysine." [ChEBI:18040, PubMed:13375629, PubMed:15504407, PubMed:16101297, PubMed:2857489, RESID:AA0028] subset: PSI-MOD_slim synonym: "(2S,5R)-2,6-diamino-5-hydroxyhexanoic acid" EXACT RESID-systematic [] synonym: "2,6-diamino-2,3,4,6-tetradeoxyhexonic acid" EXACT RESID-alternate [] synonym: "5-hydroxylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "5-hydroxylysine" EXACT UniProt-feature [] synonym: "5HyLys" EXACT PSI-MOD-short [] synonym: "alpha,epsilon-diamino-delta-hydroxycaproic acid" EXACT RESID-alternate [] synonym: "L-erythro-delta-hydroxylysine" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 6 H 12 N 2 O 2" xref: MassAvg: "144.17" xref: MassMono: "144.089878" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01047 ! monohydroxylated lysine [Term] id: MOD:00038 name: 3-hydroxy-L-proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to 3-hydroxy-L-proline." [ChEBI:16889, PubMed:2400108, PubMed:3734192, PubMed:4343807, RESID:AA0029] subset: PSI-MOD_slim synonym: "(2S,3R)-3-hydroxy-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] synonym: "3-hydroxylated L-proline" EXACT PSI-MOD-alternate [] synonym: "3-hydroxyproline" EXACT UniProt-feature [] synonym: "3-trans-hydroxy-L-proline" EXACT RESID-alternate [] synonym: "3HyPro" EXACT PSI-MOD-short [] synonym: "beta-hydroxypyrrolidine-alpha-carboxylic acid" EXACT RESID-alternate [] synonym: "L-threo-3-hydroxyproline" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 5 H 7 N 1 O 2" xref: MassAvg: "113.11" xref: MassMono: "113.047678" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01024 ! monohydroxylated proline [Term] id: MOD:00039 name: 4-hydroxy-L-proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to 4-hydroxy-L-proline" [ChEBI:18095, PubMed:11292863, PubMed:2400108, PubMed:3734192, RESID:AA0030] subset: PSI-MOD_slim synonym: "(2S,4R)-4-hydroxy-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] synonym: "4-hydroxylated L-proline" EXACT PSI-MOD-alternate [] synonym: "4-hydroxyproline" EXACT UniProt-feature [] synonym: "4-hydroxyproline" EXACT RESID-alternate [] synonym: "4-trans-hydroxy-L-proline" EXACT RESID-alternate [] synonym: "4HyPro" EXACT PSI-MOD-short [] synonym: "gamma-hydroxypyrrolidine-alpha-carboxylic acid" EXACT RESID-alternate [] synonym: "L-threo-4-hydroxyproline" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 5 H 7 N 1 O 2" xref: MassAvg: "113.11" xref: MassMono: "113.047678" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01024 ! monohydroxylated proline [Term] id: MOD:00040 name: 2-pyrrolidone-5-carboxylic acid (Gln) namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamine residue to 2-pyrrolidone-5-carboxylic acid." [ChEBI:30652, DeltaMass:123, PubMed:10214721, PubMed:1836357, PubMed:26343, PubMed:3473473, RESID:AA0031, UniMod:28] comment: DeltaMass gives a formula C 5 H 5 N 1 O 2 with mass 111.1 subset: PSI-MOD_slim synonym: "(S)-5-oxo-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] synonym: "2-oxopyrrolidine-5-carboxylic acid" EXACT RESID-alternate [] synonym: "5-oxoproline" EXACT RESID-alternate [] synonym: "5-oxopyrrolidine-2-carboxylic acid" EXACT RESID-alternate [] synonym: "Gln->pyro-Glu" RELATED PSI-MS-label [] synonym: "N-pyrrolidone carboxyl (N terminus)" EXACT DeltaMass-label [] synonym: "PyrGlu(Gln)" EXACT PSI-MOD-short [] synonym: "Pyro-glu from Q" RELATED UniMod-description [] synonym: "pyroglutamic acid" EXACT RESID-alternate [] synonym: "Pyroglutamic Acid formed from Gln" EXACT DeltaMass-label [] synonym: "Pyroglutamyl" EXACT DeltaMass-label [] synonym: "Pyrrolidone carboxylic acid" EXACT UniProt-feature [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" xref: DiffMono: "-17.026549" xref: Formula: "C 5 H 6 N 1 O 2" xref: MassAvg: "112.11" xref: MassMono: "112.039853" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00907 ! modified L-glutamine residue is_a: MOD:01048 ! 2-pyrrolidone-5-carboxylic acid is_a: MOD:01160 ! deaminated residue [Term] id: MOD:00041 name: L-gamma-carboxyglutamic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to L-gamma-carboxyglutamic acid." [DeltaMass:217, PubMed:10517147, PubMed:1807167, PubMed:3263814, PubMed:4528109, PubMed:7457858, PubMed:8135347, PubMed:8868490, PubMed:9188685, RESID:AA0032, UniMod:299] comment: DeltaMass has an incorrect formula C 6 H 7 N 5 O 1 (N and O reversed) with mass 173. subset: PSI-MOD_slim synonym: "(S)-3-amino-1,1,3-propanetricarboxylic acid" EXACT RESID-systematic [] synonym: "1-carboxyglutamic acid [misnomer]" RELATED RESID-misnomer [] synonym: "4-carboxyglutamate" EXACT UniProt-feature [] synonym: "4-carboxyglutamic acid" EXACT RESID-alternate [] synonym: "4CbxGlu" EXACT PSI-MOD-short [] synonym: "Carboxy" RELATED UniMod-interim [] synonym: "Carboxy Glutamyl" EXACT DeltaMass-label [] synonym: "Carboxylation" RELATED UniMod-description [] synonym: "gamma-carboxylated L-glutamic acid" EXACT PSI-MOD-alternate [] xref: DiffAvg: "44.01" xref: DiffFormula: "C 1 H 0 N 0 O 2" xref: DiffMono: "43.989829" xref: Formula: "C 6 H 7 N 1 O 5" xref: MassAvg: "173.12" xref: MassMono: "173.032422" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:01152 ! carboxylated residue [Term] id: MOD:00042 name: L-aspartic 4-phosphoric anhydride namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartic 4-phosphoric anhydride." [ChEBI:15836, PubMed:4357737, RESID:AA0033, UniMod:21] subset: PSI-MOD_slim synonym: "(2S)-2-amino-4-oxo-4-(phosphonooxy)butanoic acid" EXACT RESID-systematic [] synonym: "2-aminobutanedioic 4-phosphoric anhydride" EXACT RESID-alternate [] synonym: "4-aspartylphosphate" EXACT UniProt-feature [] synonym: "4-oxo-O-phosphono-L-homoserine" EXACT RESID-alternate [] synonym: "4-phosphoaspartic acid" EXACT RESID-alternate [] synonym: "4-phosphorylated L-aspartatic acid" EXACT PSI-MOD-alternate [] synonym: "beta-aspartyl phosphate" EXACT RESID-alternate [] synonym: "PhosAsp" EXACT PSI-MOD-short [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phosphorylation" RELATED UniMod-description [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 4 H 6 N 1 O 6 P 1" xref: MassAvg: "195.07" xref: MassMono: "194.993274" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00043 name: S-phospho-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-phospho-L-cysteine." [PubMed:3142516, PubMed:7961745, PubMed:8128219, RESID:AA0034, UniMod:21] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(phosphonosulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "cysteine phosphate thioester" EXACT RESID-alternate [] synonym: "PhosCys" EXACT PSI-MOD-short [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phosphocysteine" EXACT UniProt-feature [] synonym: "Phosphorylation" RELATED UniMod-description [] synonym: "S-phosphonocysteine" EXACT RESID-alternate [] synonym: "S-phosphorylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "S3-phosphocysteine" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1 S 0" xref: DiffMono: "79.966331" xref: Formula: "C 3 H 6 N 1 O 4 P 1 S 1" xref: MassAvg: "183.12" xref: MassMono: "182.975515" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00696 ! phosphorylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00044 name: 1'-phospho-L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to tele-phospho-L-histidine (N-tau-phospho-L-histidine, 1'-phospho-L-histidine)." [PubMed:11038361, PubMed:5642389, PubMed:6692818, RESID:AA0035, UniMod:21] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1-phosphono-1H-imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "histidine-3-phosphate [misnomer]" RELATED RESID-misnomer [] synonym: "histidine-N(epsilon)-phosphate" EXACT RESID-alternate [] synonym: "histidine-N1'-phosphate" EXACT RESID-alternate [] synonym: "N1-phosphonohistidine" EXACT RESID-alternate [] synonym: "NE2-phosphonohistidine" EXACT RESID-alternate [] synonym: "Ntau-phosphorylated L-histidine" EXACT PSI-MOD-alternate [] synonym: "NtauPhosHis" EXACT PSI-MOD-short [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phosphorylation" RELATED UniMod-description [] synonym: "tau-phosphohistidine" EXACT RESID-alternate [] synonym: "tele-phosphohistidine" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 6 H 8 N 3 O 4 P 1" xref: MassAvg: "217.12" xref: MassMono: "217.025242" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00890 ! phosphorylated L-histidine [Term] id: MOD:00045 name: 3'-phospho-L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to pros-phospho-L-histidine (N-pi-phospho-L-histidine, 3'-phospho-L-histidine)." [PubMed:1549615, PubMed:5642389, PubMed:6692818, PubMed:7669763, PubMed:7803390, RESID:AA0036, UniMod:21] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(3-phosphono-3H-imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "histidine-1-phosphate [misnomer]" RELATED RESID-misnomer [] synonym: "histidine-N(delta)-phosphate" EXACT RESID-alternate [] synonym: "histidine-N3'-phosphate" EXACT RESID-alternate [] synonym: "N3-phosphonohistidine" EXACT RESID-alternate [] synonym: "ND1-phosphonohistidine" EXACT RESID-alternate [] synonym: "Npi-phosphorylated L-histidine" EXACT PSI-MOD-alternate [] synonym: "NpiPhosHis" EXACT PSI-MOD-short [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phosphorylation" RELATED UniMod-description [] synonym: "pi-phosphohistidine" EXACT RESID-alternate [] synonym: "Pros-phosphohistidine" EXACT UniProt-feature [] synonym: "pros-phosphohistidine" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 6 H 8 N 3 O 4 P 1" xref: MassAvg: "217.12" xref: MassMono: "217.025242" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00890 ! phosphorylated L-histidine [Term] id: MOD:00046 name: O-phospho-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-phospho-L-serine." [ChEBI:15811, DeltaMass:0, PubMed:12923550, PubMed:4065410, PubMed:8061611, RESID:AA0037, UniMod:21] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(phosphonooxy)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-hydroxypropanoic acid 3-phosphate" EXACT RESID-alternate [] synonym: "O-phosphonoserine" EXACT RESID-alternate [] synonym: "O-phosphorylated L-serine" EXACT PSI-MOD-alternate [] synonym: "O3-phosphoserine" EXACT RESID-alternate [] synonym: "OPhosSer" EXACT PSI-MOD-short [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phospho Seryl" EXACT DeltaMass-label [] synonym: "Phosphorylation" RELATED UniMod-description [] synonym: "Phosphoserine" EXACT UniProt-feature [] synonym: "serine phosphate ester" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 3 H 6 N 1 O 5 P 1" xref: MassAvg: "167.06" xref: MassMono: "166.998359" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00047 name: O-phospho-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to O-phospho-L-threonine." [ChEBI:21967, DeltaMass:0, PubMed:12923550, PubMed:7678926, RESID:AA0038, UniMod:21] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-phosphonooxybutanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-hydroxybutanoic acid 3-phosphate" EXACT RESID-alternate [] synonym: "O-phosphorylated L-threonine" EXACT PSI-MOD-alternate [] synonym: "O3-phosphothreonine" EXACT RESID-alternate [] synonym: "OPhosThr" EXACT PSI-MOD-short [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phospho Threonyl" EXACT DeltaMass-label [] synonym: "Phosphorylation" RELATED UniMod-description [] synonym: "Phosphothreonine" EXACT UniProt-feature [] synonym: "threonine phosphate ester" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 4 H 8 N 1 O 5 P 1" xref: MassAvg: "181.08" xref: MassMono: "181.014009" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00048 name: O4'-phospho-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to O4'-phospho-L-tyrosine." [DeltaMass:0, PubMed:10226369, PubMed:1725475, RESID:AA0039, UniMod:21] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate" EXACT RESID-alternate [] synonym: "O4'-phosphorylated L-tyrosine" EXACT PSI-MOD-alternate [] synonym: "O4-phosphotyrosine" EXACT RESID-alternate [] synonym: "OPhosTyr" EXACT PSI-MOD-short [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phospho Tyrosinyl" EXACT DeltaMass-label [] synonym: "Phosphorylation" RELATED UniMod-description [] synonym: "Phosphotyrosine " EXACT UniProt-feature [] synonym: "tyrosine phosphate" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 9 H 10 N 1 O 5 P 1" xref: MassAvg: "243.15" xref: MassMono: "243.029659" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00049 name: 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to diphthamide." [ChEBI:16692, DeltaMass:122, PubMed:15316019, PubMed:7430147, RESID:AA0040, UniMod:375] subset: PSI-MOD_slim synonym: "(2R)-1-amino-4-(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-2-yl)-N,N,N-trimethyl-1-oxobutan-2-aminium" EXACT RESID-systematic [] synonym: "(3-[4-(2-amino-2-carboxy-ethyl)-1H-imidazol-2-yl]-1-carbamoyl-propyl)-trimethylammonium" EXACT RESID-alternate [] synonym: "2-[(R)-3-carboxamido-3-(trimethylammonio)propyl]-4-((S)-2-amino-2-carboxyethyl)-1H-imidazole" EXACT RESID-alternate [] synonym: "2-[3-carboxamido-3-(trimethylammonio)propyl]histidine" EXACT RESID-alternate [] synonym: "2-amino-3-[[2-(3-amino-3-carbamoyl-prop-1-enyl)-1,1,3-trimethyl-2,3-dihydroimidazol-5-yl]]propanoic acid" EXACT RESID-alternate [] synonym: "2-amino-4-[[5-(2-amino-2-carboxylato-ethyl)-1,1,3-trimethyl-2,3-dihydroimidazol-2-yl]]but-3-enamide" EXACT RESID-alternate [] synonym: "alpha-(aminocarbonyl)-4-(2-amino-2-carboxyethyl)-N,N,N-trimethyl-1H-imidazole-2-propanaminium" EXACT RESID-alternate [] synonym: "Diphth" EXACT PSI-MOD-short [] synonym: "Diphthamide" EXACT UniProt-feature [] synonym: "diphthamide" EXACT RESID-alternate [] synonym: "Diphthamide" RELATED PSI-MS-label [] synonym: "Diphthamide" RELATED UniMod-description [] synonym: "diphthamide (from histidine)" EXACT DeltaMass-label [] xref: DiffAvg: "143.21" xref: DiffFormula: "C 7 H 15 N 2 O 1" xref: DiffMono: "143.118438" xref: FormalCharge: "1+" xref: Formula: "C 13 H 22 N 5 O 2" xref: MassAvg: "280.35" xref: MassMono: "280.176801" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00050 name: N-acetyl-L-alanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to N-acetyl-L-alanine." [PubMed:363452, PubMed:4700463, RESID:AA0041] subset: PSI-MOD_slim synonym: "(S)-2-(acetamido)propanoic acid" EXACT RESID-systematic [] synonym: "2-(acetylamino)propanoic acid" EXACT RESID-alternate [] synonym: "AcAla" EXACT PSI-MOD-short [] synonym: "acetylalanine" EXACT RESID-alternate [] synonym: "N-acetylalanine" EXACT UniProt-feature [] synonym: "N-acetylated L-alanine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 5 H 8 N 1 O 2" xref: MassAvg: "114.12" xref: MassMono: "114.055504" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00901 ! modified L-alanine residue [Term] id: MOD:00051 name: N-acetyl-L-aspartic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to N-acetyl-L-aspartic acid." [ChEBI:21547, PubMed:1560020, PubMed:2395459, RESID:AA0042] subset: PSI-MOD_slim synonym: "(S)-2-(acetamido)butanedioic acid" EXACT RESID-systematic [] synonym: "2-(acetylamino)butanedioic acid" EXACT RESID-alternate [] synonym: "AcAsp" EXACT PSI-MOD-short [] synonym: "acetylaspartic acid" EXACT RESID-alternate [] synonym: "N-acetylaspartate" EXACT UniProt-feature [] synonym: "N-acetylated L-aspartic acid" EXACT PSI-MOD-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 6 H 8 N 1 O 4" xref: MassAvg: "158.13" xref: MassMono: "158.045333" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00052 name: N-acetyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to N-acetyl-L-cysteine." [ChEBI:28939, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:1500421, PubMed:15350136, PubMed:6725286, RESID:AA0043] comment: incidental to RESID:AA0223 subset: PSI-MOD_slim synonym: "(R)-2-acetamido-3-sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-3-mercaptopropanoic acid" EXACT RESID-alternate [] synonym: "2-acetylamino-3-sulfanylpropanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "N-acetylated cysteine" EXACT PSI-MOD-alternate [] synonym: "N-acetylcysteine" EXACT UniProt-feature [] synonym: "N-acetylcysteine" EXACT RESID-alternate [] synonym: "NAcCys" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1 S 0" xref: DiffMono: "42.010565" xref: Formula: "C 5 H 8 N 1 O 2 S 1" xref: MassAvg: "146.19" xref: MassMono: "146.027574" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00646 ! acetylated L-cysteine [Term] id: MOD:00053 name: N-acetyl-L-glutamic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to N-acetyl-L-glutamic acid." [ChEBI:17533, PubMed:6725286, RESID:AA0044] subset: PSI-MOD_slim synonym: "(S)-2-(acetamido)pentanedioic acid" EXACT RESID-systematic [] synonym: "2-(acetylamino)pentanedioic acid" EXACT RESID-alternate [] synonym: "acetylglutamic acid" EXACT RESID-alternate [] synonym: "AcGlu" EXACT PSI-MOD-short [] synonym: "N-acetylated L-glutamic acid" EXACT PSI-MOD-alternate [] synonym: "N-acetylglutamate" EXACT UniProt-feature [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 7 H 10 N 1 O 4" xref: MassAvg: "172.16" xref: MassMono: "172.060983" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00054 name: N-acetyl-L-glutamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamine residue to N-acetyl-L-glutamine." [RESID:AA0045] subset: PSI-MOD_slim synonym: "(S)-2-acetamido-5-pentanediamic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-5-pentanediamic acid" EXACT RESID-alternate [] synonym: "acetylglutamine" EXACT RESID-alternate [] synonym: "AcGln" EXACT PSI-MOD-short [] synonym: "N-acetylated L-glutamine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 7 H 11 N 2 O 3" xref: MassAvg: "171.17" xref: MassMono: "171.076967" xref: Origin: "Q" xref: Source: "artifact" xref: TermSpec: "N-term" is_a: MOD:00907 ! modified L-glutamine residue [Term] id: MOD:00055 name: N-acetylglycine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-acetylglycine." [PubMed:272676, PubMed:5545094, PubMed:6754709, RESID:AA0046] subset: PSI-MOD_slim synonym: "2-(acetamido)ethanoic acid" EXACT RESID-systematic [] synonym: "2-(acetylamino)ethanoic acid" EXACT RESID-alternate [] synonym: "aceturic acid" EXACT RESID-alternate [] synonym: "AcGly" EXACT PSI-MOD-short [] synonym: "N-acetylated glycine" EXACT PSI-MOD-alternate [] synonym: "N-acetylglycine" EXACT UniProt-feature [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 4 H 6 N 1 O 2" xref: MassAvg: "100.10" xref: MassMono: "100.039853" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00056 name: N-acetyl-L-isoleucine namespace: PSI-MOD def: "A protein modification that effectively converts an L-isoleucine residue to N-acetyl-L-isoleucine." [PubMed:8034631, RESID:AA0047] comment: This modification has not been observed to occur naturally. subset: PSI-MOD_slim synonym: "(2S,3S)-2-acetamido-3-methylpentanoic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-3-methylpentanoic acid" EXACT RESID-alternate [] synonym: "acetylisoleucine" EXACT RESID-alternate [] synonym: "AcIle" EXACT PSI-MOD-short [] synonym: "N-acetylated L-isoleucine" EXACT PSI-MOD-alternate [] synonym: "N-acetylisoleucine" EXACT UniProt-feature [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 8 H 14 N 1 O 2" xref: MassAvg: "156.20" xref: MassMono: "156.102454" xref: Origin: "I" xref: Source: "artifact" xref: TermSpec: "N-term" is_a: MOD:00910 ! modified L-isoleucine residue [Term] id: MOD:00057 name: N2-acetyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N2-acetyl-L-lysine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, RESID:AA0048] comment: This modification has not been observed to occur naturally. subset: PSI-MOD_slim synonym: "(S)-2-acetamido-6-aminohexanoic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-6-aminohexanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "N2-acetylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N2-acetyllysine" EXACT RESID-alternate [] synonym: "N2AcLys" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 8 H 15 N 2 O 2" xref: MassAvg: "171.22" xref: MassMono: "171.113353" xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "N-term" is_a: MOD:00723 ! N-acetylated L-lysine [Term] id: MOD:00058 name: N-acetyl-L-methionine namespace: PSI-MOD def: "A protein modification that effectively converts an L-methionine to N-acetyl-L-methionine." [PubMed:7944406, RESID:AA0049] subset: PSI-MOD_slim synonym: "(S)-2-acetamido-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-4-(methylsulfanyl)butanoic acid" EXACT RESID-alternate [] synonym: "2-acetylamino-4-(methylthio)butanoic acid" EXACT RESID-alternate [] synonym: "acetylmethionine" EXACT RESID-alternate [] synonym: "AcMet" EXACT PSI-MOD-short [] synonym: "methionamine" EXACT RESID-alternate [] synonym: "N-acetylated L-methionine" EXACT PSI-MOD-alternate [] synonym: "N-acetylmethionine" EXACT UniProt-feature [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1 S 0" xref: DiffMono: "42.010565" xref: Formula: "C 7 H 12 N 1 O 2 S 1" xref: MassAvg: "174.24" xref: MassMono: "174.058875" xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00059 name: N-acetyl-L-proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to N-acetyl-L-proline." [PubMed:2928307, RESID:AA0050] subset: PSI-MOD_slim synonym: "(2S)-1-acetyl-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] synonym: "1-acetylproline [misnomer]" RELATED RESID-misnomer [] synonym: "acetylproline" EXACT RESID-alternate [] synonym: "N-acetylated L-proline" EXACT PSI-MOD-alternate [] synonym: "N-acetylproline" EXACT UniProt-feature [] synonym: "N-acetylproline" EXACT RESID-alternate [] synonym: "NAcPro" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 7 H 10 N 1 O 2" xref: MassAvg: "140.16" xref: MassMono: "140.071154" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00060 name: N-acetyl-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to N-acetyl-L-serine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:1880797, PubMed:2106685, PubMed:6997045, RESID:AA0051] subset: PSI-MOD_slim synonym: "(S)-2-acetamido-3-hydroxypropanoic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-3-hydroxypropanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "N-acetylated L-serine" EXACT PSI-MOD-alternate [] synonym: "N-acetylserine" EXACT UniProt-feature [] synonym: "N-acetylserine" EXACT RESID-alternate [] synonym: "NAcSer" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 5 H 8 N 1 O 3" xref: MassAvg: "130.12" xref: MassMono: "130.050418" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00647 ! acetylated L-serine [Term] id: MOD:00061 name: N-acetyl-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to N-acetyl-L-threonine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:2106685, PubMed:6997045, RESID:AA0052] subset: PSI-MOD_slim synonym: "(2S,3R)-2-acetamido-3-hydroxybutanoic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-3-hydroxybutanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "Acetylation" RELATED UniMod-description [] synonym: "N-acetylated L-threonine" EXACT PSI-MOD-alternate [] synonym: "N-acetylthreonine" EXACT UniProt-feature [] synonym: "N-acetylthreonine" EXACT RESID-alternate [] synonym: "NAcThr" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 6 H 10 N 1 O 3" xref: MassAvg: "144.15" xref: MassMono: "144.066068" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:01186 ! acetylated L-threonine [Term] id: MOD:00062 name: N-acetyl-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to N-acetyl-L-tyrosine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:2506074, PubMed:475783, RESID:AA0053] subset: PSI-MOD_slim synonym: "(S)-2-acetamido-3-(4-hydoxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-3-(4-hydoxyphenyl)propanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "AcTyr" EXACT PSI-MOD-short [] synonym: "N-acetylated L-tyrosine" EXACT PSI-MOD-alternate [] synonym: "N-acetyltyrosine" EXACT UniProt-feature [] synonym: "N-acetyltyrosine" EXACT RESID-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 11 H 12 N 1 O 3" xref: MassAvg: "206.22" xref: MassMono: "206.081718" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00063 name: N-acetyl-L-valine namespace: PSI-MOD def: "A protein modification that effectively converts an L-valine residue to N-acetyl-L-valine." [PubMed:1735421, RESID:AA0054] subset: PSI-MOD_slim synonym: "(S)-2-acetamido-3-methylbutanoic acid" EXACT RESID-systematic [] synonym: "2-acetylamino-3-methylbutanoic acid" EXACT RESID-alternate [] synonym: "AcVal" EXACT PSI-MOD-short [] synonym: "N-acetylated L-valine" EXACT PSI-MOD-alternate [] synonym: "N-acetylvaline" EXACT UniProt-feature [] synonym: "N-acetylvaline" EXACT RESID-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 7 H 12 N 1 O 2" xref: MassAvg: "142.18" xref: MassMono: "142.086804" xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00920 ! modified L-valine residue [Term] id: MOD:00064 name: N6-acetyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-acetyl-L-lysine." [ChEBI:17752, DeltaMass:214, PubMed:11369851, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:1680872, PubMed:670159, RESID:AA0055, UniMod:1] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-acetamidohexanoic acid" EXACT RESID-systematic [] synonym: "2-amino-6-acetylaminohexanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "Acetylation" RELATED UniMod-description [] synonym: "epsilon-acetyllysine" EXACT RESID-alternate [] synonym: "N(zeta)-acetyllysine" EXACT RESID-alternate [] synonym: "N6-acetylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6-acetyllysine" EXACT UniProt-feature [] synonym: "N6AcLys" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 8 H 14 N 2 O 2" xref: MassAvg: "170.21" xref: MassMono: "170.105528" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00723 ! N-acetylated L-lysine [Term] id: MOD:00065 name: S-acetyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-acetyl-L-cysteine." [PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:1310545, PubMed:14730666, PubMed:15350136, RESID:AA0056, UniMod:1] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(acetylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(acetylthio)propanoic acid" EXACT RESID-alternate [] synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "Acetylation" RELATED UniMod-description [] synonym: "cysteine acetate thioester" EXACT RESID-alternate [] synonym: "S-acetylcysteine" EXACT RESID-alternate [] synonym: "SAcCys" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1 S 0" xref: DiffMono: "42.010565" xref: Formula: "C 5 H 7 N 1 O 2 S 1" xref: MassAvg: "145.18" xref: MassMono: "145.019749" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00645 ! S-acetylated residue is_a: MOD:00646 ! acetylated L-cysteine [Term] id: MOD:00066 name: N-formylglycine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-formylglycine." [PubMed:5139483, RESID:AA0057] subset: PSI-MOD_slim synonym: "formylaminoethanoic acid" EXACT RESID-systematic [] synonym: "N(alpha)-formylglycine" EXACT RESID-alternate [] synonym: "N-formylated glycine" EXACT PSI-MOD-alternate [] synonym: "N-formylglycine" EXACT UniProt-feature [] synonym: "NFoGly" EXACT PSI-MOD-short [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 H 0 N 0 O 1" xref: DiffMono: "27.994915" xref: Formula: "C 3 H 4 N 1 O 2" xref: MassAvg: "86.07" xref: MassMono: "86.024203" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00409 ! N-formylated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00067 name: N-D-glucuronoylglycine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-D-glucuronoylglycine." [PubMed:10858503, PubMed:12716131, PubMed:6493057, PubMed:7398618, RESID:AA0058, UniMod:54] subset: PSI-MOD_slim synonym: "NGlcAGly" EXACT PSI-MOD-short [] xref: DiffAvg: "176.12" xref: DiffFormula: "C 6 H 8 N 0 O 6" xref: DiffMono: "176.032088" xref: Formula: "C 8 H 12 N 1 O 7" xref: MassAvg: "234.18" xref: MassMono: "234.061377" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00447 ! N-glucuronylated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00068 name: N-myristoylglycine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-myristoylglycine." [PubMed:11955007, PubMed:11955008, PubMed:1326520, PubMed:1386601, PubMed:6436247, PubMed:7543369, RESID:AA0059, UniMod:45] subset: PSI-MOD_slim synonym: "(tetradecanoylamino)ethanoic acid" EXACT RESID-systematic [] synonym: "Myristoyl" RELATED PSI-MS-label [] synonym: "Myristoylation" RELATED UniMod-description [] synonym: "N-(1-oxotetradecyl)glycine" EXACT RESID-alternate [] synonym: "N-myristoyl glycine" EXACT UniProt-feature [] synonym: "N-myristoylated glycine" EXACT PSI-MOD-alternate [] synonym: "N-myristylglycine" EXACT RESID-alternate [] synonym: "N-tetradecanoylglycine" EXACT RESID-alternate [] synonym: "NMyrGly" EXACT PSI-MOD-short [] xref: DiffAvg: "210.36" xref: DiffFormula: "C 14 H 26 N 0 O 1" xref: DiffMono: "210.198365" xref: Formula: "C 16 H 30 N 1 O 2" xref: MassAvg: "268.41" xref: MassMono: "268.227654" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00650 ! N-myristoylated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00069 name: N-palmitoyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to N-palmitoyl-L-cysteine." [PubMed:10896212, PubMed:4575979, PubMed:9056182, PubMed:9593755, RESID:AA0060, UniMod:47] comment: incidental to RESID:AA0107 incidental to RESID:AA0309 subset: PSI-MOD_slim synonym: "(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-hexadecanoylamino-3-mercaptopropanoic acid" EXACT RESID-alternate [] synonym: "N-(1-oxahexadecyl)-L-cysteine" EXACT RESID-alternate [] synonym: "N-palmitoyl cysteine" EXACT UniProt-feature [] synonym: "N-palmitoylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "NPamCys" EXACT PSI-MOD-short [] synonym: "Palmitoyl" RELATED PSI-MS-label [] synonym: "Palmitoylation" RELATED UniMod-description [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1 S 0" xref: DiffMono: "238.229666" xref: Formula: "C 19 H 36 N 1 O 2 S 1" xref: MassAvg: "342.56" xref: MassMono: "342.246675" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00651 ! N-palmitoylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00070 name: N-methyl-L-alanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to N-methyl-L-alanine." [ChEBI:17519, PubMed:323502, PubMed:337304, PubMed:7007074, RESID:AA0061] subset: PSI-MOD_slim synonym: "(S)-2-methylaminopropanoic acid" EXACT RESID-systematic [] synonym: "N-methylalanine" EXACT UniProt-feature [] synonym: "N-methylalanine" EXACT RESID-alternate [] synonym: "N-methylated L-alanine" EXACT PSI-MOD-alternate [] synonym: "NMeAla" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 4 H 7 N 1 O 1" xref: MassAvg: "85.10" xref: MassMono: "85.052764" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00599 ! monomethylated residue [Term] id: MOD:00071 name: N,N,N-trimethyl-L-alanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to N,N,N-trimethyl-L-alanine." [PubMed:12590383, PubMed:332162, PubMed:3979397, PubMed:6778808, PubMed:7715456, RESID:AA0062, UniMod:37] subset: PSI-MOD_slim synonym: "(S)-1-carboxy-N,N,N-trimethylethanaminium" EXACT RESID-alternate [] synonym: "(S)-2-(trimethylammonio)propanoic acid" EXACT RESID-systematic [] synonym: "N,N,N-trimethylalanine" EXACT UniProt-feature [] synonym: "N,N,N-trimethylated L-alanine" EXACT PSI-MOD-alternate [] synonym: "NMe3Ala" EXACT PSI-MOD-short [] synonym: "tri-Methylation" RELATED UniMod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] xref: DiffAvg: "43.09" xref: DiffFormula: "C 3 H 7 N 0 O 0" xref: DiffMono: "43.054775" xref: FormalCharge: "1+" xref: Formula: "C 6 H 13 N 1 O 1" xref: MassAvg: "115.17" xref: MassMono: "115.099165" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00430 ! trimethylated residue is_a: MOD:00711 ! protonated-trimethylated residue [Term] id: MOD:00072 name: N-methylglycine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-methylglycine." [ChEBI:15611, DeltaMass:0, PubMed:1593629, RESID:AA0063] comment: DeltaMass also has an entry for the free amino acid subset: PSI-MOD_slim synonym: "L-sarcosine" EXACT RESID-alternate [] synonym: "methylaminoacetic acid" EXACT RESID-alternate [] synonym: "methylaminoethanoic acid" EXACT RESID-systematic [] synonym: "N-methylated glycine" EXACT PSI-MOD-alternate [] synonym: "NMeGly" EXACT PSI-MOD-short [] synonym: "Sar" EXACT DeltaMass-label [] synonym: "Sarcosine" EXACT DeltaMass-label [] synonym: "Sarcosyl" EXACT DeltaMass-label [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 3 H 5 N 1 O 1" xref: MassAvg: "71.08" xref: MassMono: "71.037114" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00714 ! methylated glycine [Term] id: MOD:00073 name: N-methyl-L-methionine namespace: PSI-MOD def: "A protein modification that effectively converts an L-methionine residue to N-methyl-L-methionine." [DeltaMass:169, PubMed:323502, PubMed:3298225, RESID:AA0064] subset: PSI-MOD_slim synonym: "(S)-2-methylamino-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-methylamino-4-(methylthio)butanoic acid" EXACT RESID-alternate [] synonym: "Methyl Methionyl" EXACT DeltaMass-label [] synonym: "N-methylated L-methionine" EXACT PSI-MOD-alternate [] synonym: "N-methylmethionine" EXACT UniProt-feature [] synonym: "N-methylmethionine" EXACT RESID-alternate [] synonym: "NMeMet" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 0" xref: DiffMono: "14.015650" xref: Formula: "C 6 H 11 N 1 O 1 S 1" xref: MassAvg: "145.22" xref: MassMono: "145.056135" xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue [Term] id: MOD:00074 name: N-methyl-L-phenylalanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-phenylalanine residue to N-methyl-L-phenylalanine." [PubMed:2577730, PubMed:413571, RESID:AA0065] subset: PSI-MOD_slim synonym: "(S)-2-methylamino-3-phenylpropanoic acid" EXACT RESID-systematic [] synonym: "N-methylated L-phenylalanine" EXACT PSI-MOD-alternate [] synonym: "N-methylphenylalanine" EXACT UniProt-feature [] synonym: "N-methylphenylalanine" EXACT RESID-alternate [] synonym: "NMePhe" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 10 H 11 N 1 O 1" xref: MassAvg: "161.20" xref: MassMono: "161.084064" xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00717 ! methylated phenylalanine [Term] id: MOD:00075 name: N,N-dimethyl-L-proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to N,N-dimethyl-L-proline." [ChEBI:21451, PubMed:12964758, PubMed:14570711, PubMed:193025, PubMed:3882426, PubMed:6254758, RESID:AA0066, UniMod:529] comment: UniMod terminal specification corrected. [JSG] subset: PSI-MOD_slim synonym: "(S)-2-carboxy-1,1-dimethylpyrrolidinium" EXACT RESID-systematic [] synonym: "(S)-2-carboxy-1,1-dimethylpyrrolidinium" EXACT RESID-alternate [] synonym: "1,1-dimethyl-L-prolinium [misnomer]" RELATED RESID-misnomer [] synonym: "Delta:H(5)C(2)" RELATED UniMod-label [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "Dimethylation of proline residue" RELATED UniMod-description [] synonym: "N,N-dimethyl-L-prolinium" EXACT RESID-alternate [] synonym: "N,N-dimethylated L-proline" EXACT PSI-MOD-alternate [] synonym: "N,N-dimethylproline" EXACT UniProt-feature [] synonym: "NMe2Pro" EXACT PSI-MOD-short [] synonym: "stachydrin" EXACT RESID-alternate [] xref: DiffAvg: "29.06" xref: DiffFormula: "C 2 H 5 N 0 O 0" xref: DiffMono: "29.039125" xref: FormalCharge: "1+" xref: Formula: "C 7 H 13 N 1 O 1" xref: MassAvg: "127.18" xref: MassMono: "127.099165" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00710 ! protonated-dimethylated residue is_a: MOD:01462 ! N-alpha-methylated proline [Term] id: MOD:00076 name: omega-N,omega-N'-dimethyl-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to N(omega),N'(omega)-dimethyl-L-arginine." [PubMed:12964758, PubMed:14570711, PubMed:15835918, PubMed:2426402, PubMed:5128665, RESID:AA0067, UniMod:36] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-[((methylamino)(methylimino)methyl)amino]pentanoic acid" EXACT RESID-systematic [] synonym: "di-Methylation" RELATED UniMod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "N3,N4-dimethylarginine" EXACT RESID-alternate [] synonym: "N5-[(methylamino)(methylimino)methyl]ornithine" EXACT RESID-alternate [] synonym: "NG,N'G-dimethylarginine" EXACT RESID-alternate [] synonym: "NoNo'Me2Arg" EXACT PSI-MOD-short [] synonym: "omega-N,omega-N'-dimethylated L-arginine" EXACT PSI-MOD-alternate [] synonym: "Symmetric dimethylarginine" EXACT UniProt-feature [] synonym: "symmetric dimethylarginine" EXACT RESID-alternate [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4 N 0 O 0" xref: DiffMono: "28.031300" xref: Formula: "C 8 H 16 N 4 O 1" xref: MassAvg: "184.24" xref: MassMono: "184.132411" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00783 ! dimethylated L-arginine [Term] id: MOD:00077 name: omega-N,omega-N-dimethyl-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to N(omega),N(omega)-dimethyl-L-arginine." [ChEBI:17929, PubMed:11152131, PubMed:12964758, PubMed:14570711, PubMed:15835918, PubMed:3032834, RESID:AA0068, UniMod:36] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-([(dimethylamino)(imino)methyl]amino)pentanoic acid" EXACT RESID-systematic [] synonym: "Asymmetric dimethylarginine" EXACT UniProt-feature [] synonym: "asymmetric dimethylarginine" EXACT RESID-alternate [] synonym: "di-Methylation" RELATED UniMod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "N5-[(dimethylamino)(imino)methyl]ornithine" EXACT RESID-alternate [] synonym: "NG,NG-dimethylarginine" EXACT RESID-alternate [] synonym: "NoNoMe2Arg" EXACT PSI-MOD-short [] synonym: "omega-N,omega-N-dimethlyated L-arginine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4 N 0 O 0" xref: DiffMono: "28.031300" xref: Formula: "C 8 H 16 N 4 O 1" xref: MassAvg: "184.24" xref: MassMono: "184.132411" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00783 ! dimethylated L-arginine [Term] id: MOD:00078 name: omega-N-methyl-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to N(omega)-methyl-L-arginine." [PubMed:11875433, PubMed:15835918, PubMed:2426402, PubMed:5128665, RESID:AA0069, UniMod:34] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid" EXACT RESID-systematic [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "NG-methylarginine" EXACT RESID-alternate [] synonym: "NoMeArg" EXACT PSI-MOD-short [] synonym: "Omega-N-methylarginine" EXACT UniProt-feature [] synonym: "omega-N-methylated L-arginine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 14 N 4 O 1" xref: MassAvg: "170.21" xref: MassMono: "170.116761" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00414 ! monomethylated L-arginine is_a: MOD:00602 ! N-methylated residue [Term] id: MOD:00079 name: N4-methyl-L-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to N4-methyl-L-asparagine." [PubMed:11875433, PubMed:2356973, PubMed:3782095, RESID:AA0070, UniMod:34] subset: PSI-MOD_slim synonym: "(S)-2-amino-N4-methylbutanediamic acid" EXACT RESID-systematic [] synonym: "beta-methylasparagine [misnomer]" RELATED RESID-misnomer [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "N(gamma)-methylasparagine" EXACT RESID-alternate [] synonym: "N-methylasparagine" EXACT RESID-alternate [] synonym: "N4-methylasparagine" EXACT UniProt-feature [] synonym: "N4-methylated L-asparagine" EXACT PSI-MOD-alternate [] synonym: "N4MeAsn" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 5 H 8 N 2 O 2" xref: MassAvg: "128.13" xref: MassMono: "128.058578" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00673 ! methylated asparagine [Term] id: MOD:00080 name: N5-methyl-L-glutamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamine residue to N5-methyl-L-glutamine." [ChEBI:17592, DeltaMass:166, PubMed:11118225, PubMed:11875433, PubMed:365579, RESID:AA0071, UniMod:34] subset: PSI-MOD_slim synonym: "(2S)-2-amino-5-methylamino-5-oxopentanoic acid" EXACT RESID-systematic [] synonym: "2-amino-N5-methylpentanediamic acid" EXACT RESID-alternate [] synonym: "gamma-methylglutamine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "N(delta)-methylglutamine" EXACT RESID-alternate [] synonym: "N-methylglutamine" EXACT RESID-alternate [] synonym: "N5-methylated L-glutamine" EXACT PSI-MOD-alternate [] synonym: "N5-methylglutamine" EXACT UniProt-feature [] synonym: "N5MeGln" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 6 H 10 N 2 O 2" xref: MassAvg: "142.16" xref: MassMono: "142.074228" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00722 ! monomethylated L-glutamine [Term] id: MOD:00081 name: L-glutamic acid 5-methyl ester (Glu) namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamate 5-methyl ester." [DeltaMass:167, PubMed:16888, PubMed:6300110, RESID:AA0072, UniMod:34] comment: DeltaMass gives the formula "C 6 H 9 O 1 N 3" with mass 143 [JSG]. subset: PSI-MOD_slim synonym: "5-methyl esterified L-glutamic acid" EXACT PSI-MOD-alternate [] synonym: "Glutamate methyl ester (Glu)" EXACT UniProt-feature [] synonym: "O-methyl Glutamyl" EXACT DeltaMass-label [] synonym: "O5MeGlu" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 6 H 9 N 1 O 3" xref: MassAvg: "143.14" xref: MassMono: "143.058243" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01453 ! L-glutamic acid 5-methyl ester [Term] id: MOD:00082 name: 3'-methyl-L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to pros-methyl-L-histidine (N-pi-methyl-L-histidine, 3'-methyl-L-histidine)." [PubMed:10660523, PubMed:11875433, PubMed:3467365, PubMed:6692818, PubMed:8076, PubMed:8645219, RESID:AA0073, UniMod:34] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(3-methyl-3H-imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "1-methylhistidine [misnomer]" RELATED RESID-misnomer [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "N(delta)-methylhistidine" EXACT RESID-alternate [] synonym: "NprosMeHis" EXACT PSI-MOD-short [] synonym: "pi-methylhistidine" EXACT RESID-alternate [] synonym: "pros-methylated L-histidine" EXACT PSI-MOD-alternate [] synonym: "Pros-methylhistidine" EXACT UniProt-feature [] synonym: "pros-methylhistidine" EXACT RESID-alternate [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 9 N 3 O 1" xref: MassAvg: "151.17" xref: MassMono: "151.074562" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00724 ! N-methylated L-histidine [Term] id: MOD:00083 name: N6,N6,N6-trimethyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6,N6,N6-trimethyl-L-lysine." [ChEBI:17311, DeltaMass:0, PubMed:12590383, PubMed:3145979, PubMed:4304194, PubMed:6778808, PubMed:7093227, PubMed:8453381, RESID:AA0074, UniMod:37] comment: DeltaMass calculates the mass difference from protonated lysine rather than neutral lysine subset: PSI-MOD_slim synonym: "(S)-2-amino-6-(trimethylammonio)hexanoic acid" EXACT RESID-systematic [] synonym: "(S)-5-amino-5-carboxy-N,N,N-trimethyl-1-pentanaminium" EXACT RESID-alternate [] synonym: "epsilon-trimethyllysine" EXACT RESID-alternate [] synonym: "N(zeta)-trimethyllysine" EXACT RESID-alternate [] synonym: "N-trimethylation (of lysine)" EXACT DeltaMass-label [] synonym: "N6,N6,N6-trimethylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6,N6,N6-trimethyllysin-N6-ium" EXACT RESID-alternate [] synonym: "N6,N6,N6-trimethyllysine" EXACT UniProt-feature [] synonym: "N6Me3Lys" EXACT PSI-MOD-short [] synonym: "tri-Methylation" RELATED UniMod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] xref: DiffAvg: "43.09" xref: DiffFormula: "C 3 H 7 N 0 O 0" xref: DiffMono: "43.054775" xref: FormalCharge: "1+" xref: Formula: "C 9 H 19 N 2 O 1" xref: MassAvg: "171.26" xref: MassMono: "171.149190" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00430 ! trimethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00663 ! methylated lysine is_a: MOD:00711 ! protonated-trimethylated residue [Term] id: MOD:00084 name: N6,N6-dimethyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6,N6-dimethyl-L-lysine." [PubMed:10550045, PubMed:12964758, PubMed:14570711, PubMed:3100523, PubMed:8453381, RESID:AA0075, UniMod:36] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-dimethylaminohexanoic acid" EXACT RESID-systematic [] synonym: "di-Methylation" RELATED UniMod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "epsilon-dimethyllysine" EXACT RESID-alternate [] synonym: "lysine derivative Lys(y)" EXACT RESID-alternate [] synonym: "N(zeta)-dimethyllysine" EXACT RESID-alternate [] synonym: "N6,N6-dimethylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6,N6-dimethyllysine" EXACT UniProt-feature [] synonym: "N6Me2Lys" EXACT PSI-MOD-short [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4 N 0 O 0" xref: DiffMono: "28.031300" xref: Formula: "C 8 H 16 N 2 O 1" xref: MassAvg: "156.23" xref: MassMono: "156.126263" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00429 ! dimethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00663 ! methylated lysine [Term] id: MOD:00085 name: N6-methyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-methyl-L-lysine." [ChEBI:17604, DeltaMass:165, PubMed:11875433, PubMed:3926756, RESID:AA0076, UniMod:34] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-methylaminohexanoic acid" EXACT RESID-systematic [] synonym: "epsilon-methyllysine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "N(zeta)-methyllysine" EXACT RESID-alternate [] synonym: "N-methyl Lysyl" EXACT DeltaMass-label [] synonym: "N6-methylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6-methyllysine" EXACT UniProt-feature [] synonym: "N6MeLys" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 14 N 2 O 1" xref: MassAvg: "142.20" xref: MassMono: "142.110613" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00663 ! methylated lysine [Term] id: MOD:00086 name: N6-palmitoyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-palmitoyl-L-lysine." [PubMed:2498336, PubMed:7801126, PubMed:7939682, RESID:AA0077, UniMod:47] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-(hexadecanoylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "epsilon-palmitoyllysine" EXACT RESID-alternate [] synonym: "N(zeta)-palmitoyllysine" EXACT RESID-alternate [] synonym: "N6-(1-oxohexadecyl)-L-lysine" EXACT RESID-alternate [] synonym: "N6-palmitoyl lysine" EXACT UniProt-feature [] synonym: "N6-palmitoylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6PamLys" EXACT PSI-MOD-short [] synonym: "Palmitoyl" RELATED PSI-MS-label [] synonym: "Palmitoylation" RELATED UniMod-description [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1" xref: DiffMono: "238.229666" xref: Formula: "C 22 H 42 N 2 O 2" xref: MassAvg: "366.58" xref: MassMono: "366.324629" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00651 ! N-palmitoylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00087 name: N6-myristoyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-myristoyl-L-lysine." [PubMed:1402651, PubMed:8346241, RESID:AA0078, UniMod:45] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-(tetradecanoylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "epsilon-myristoyllysine" EXACT RESID-alternate [] synonym: "Myristoyl" RELATED PSI-MS-label [] synonym: "Myristoylation" RELATED UniMod-description [] synonym: "N(zeta)-myristoyllysine" EXACT RESID-alternate [] synonym: "N6-(1-oxotetradecyl)-L-lysine" EXACT RESID-alternate [] synonym: "N6-myristoyl lysine" EXACT UniProt-feature [] synonym: "N6-myristoylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6MyrLys" EXACT PSI-MOD-short [] xref: DiffAvg: "210.36" xref: DiffFormula: "C 14 H 26 N 0 O 1" xref: DiffMono: "210.198365" xref: Formula: "C 20 H 38 N 2 O 2" xref: MassAvg: "338.53" xref: MassMono: "338.293328" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00650 ! N-myristoylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00088 name: O-palmitoyl-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to O-palmitoyl-L-threonine." [PubMed:6642431, PubMed:8413602, RESID:AA0079, UniMod:47] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-(hexadecanoyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "L-threonine hexadecanoate ester" EXACT RESID-alternate [] synonym: "O-palmitoyl threonine" EXACT UniProt-feature [] synonym: "O-palmitoylated L-threonine" EXACT PSI-MOD-alternate [] synonym: "O3-palmitoyl-threonine" EXACT RESID-alternate [] synonym: "OPamThr" EXACT PSI-MOD-short [] synonym: "Palmitoyl" RELATED PSI-MS-label [] synonym: "Palmitoylation" RELATED UniMod-description [] synonym: "threonine palmitate ester" EXACT RESID-alternate [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1" xref: DiffMono: "238.229666" xref: Formula: "C 20 H 37 N 1 O 3" xref: MassAvg: "339.51" xref: MassMono: "339.277344" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00652 ! O-palmitoylated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00089 name: O-palmitoyl-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-palmitoyl-L-serine." [PubMed:3467339, RESID:AA0080, UniMod:47] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-(hexadecanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "L-serine hexadecanoate ester" EXACT RESID-alternate [] synonym: "O-palmitoyl serine" EXACT UniProt-feature [] synonym: "O-palmitoylated L-serine" EXACT PSI-MOD-alternate [] synonym: "O3-palmitoyl-serine" EXACT RESID-alternate [] synonym: "OPamSer" EXACT PSI-MOD-short [] synonym: "Palmitoyl" RELATED PSI-MS-label [] synonym: "Palmitoylation" RELATED UniMod-description [] synonym: "serine palmitate ester" EXACT RESID-alternate [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1" xref: DiffMono: "238.229666" xref: Formula: "C 19 H 35 N 1 O 3" xref: MassAvg: "325.49" xref: MassMono: "325.261694" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00652 ! O-palmitoylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00090 name: L-alanine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to L-alanine amide." [PubMed:1377792, PubMed:2069951, PubMed:8472537, PubMed:952951, RESID:AA0081] subset: PSI-MOD_slim synonym: "(S)-2-aminopropanamide" EXACT RESID-systematic [] synonym: "AlaN" EXACT PSI-MOD-short [] synonym: "alaninamide" EXACT RESID-alternate [] synonym: "Alanine amide" EXACT UniProt-feature [] synonym: "amidated L-alanine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 3 H 7 N 2 O 1" xref: MassAvg: "87.10" xref: MassMono: "87.055838" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00901 ! modified L-alanine residue [Term] id: MOD:00091 name: L-arginine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to L-arginine amide." [PubMed:2229025, PubMed:2753890, PubMed:743209, RESID:AA0082] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-carbamimidamidopentanamide" EXACT RESID-systematic [] synonym: "2-amino-5-guanidinopentanamide" EXACT RESID-alternate [] synonym: "amidated L-arginine" EXACT PSI-MOD-alternate [] synonym: "argininamide" EXACT RESID-alternate [] synonym: "Arginine amide" EXACT UniProt-feature [] synonym: "ArgN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 6 H 14 N 5 O 1" xref: MassAvg: "172.21" xref: MassMono: "172.119835" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00092 name: L-asparagine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to L-asparagine amide." [PubMed:2753132, PubMed:279902, PubMed:3415690, RESID:AA0083] subset: PSI-MOD_slim synonym: "(S)-2-amino-butanediamide" EXACT RESID-systematic [] synonym: "amidated L-asparagine" EXACT PSI-MOD-alternate [] synonym: "AsnN" EXACT PSI-MOD-short [] synonym: "asparaginamide" EXACT RESID-alternate [] synonym: "Asparagine amide" EXACT UniProt-feature [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 4 H 8 N 3 O 2" xref: MassAvg: "130.13" xref: MassMono: "130.061652" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00093 name: L-aspartic acid 1-amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartic acid 1-amide." [PubMed:2542051, RESID:AA0084] subset: PSI-MOD_slim synonym: "(S)-2-amino-1-butanediamic acid" EXACT RESID-systematic [] synonym: "1-amidated L-aspartic acid" EXACT PSI-MOD-alternate [] synonym: "3,4-diamino-4-oxabutanoic acid" EXACT RESID-alternate [] synonym: "Aspartic acid 1-amide" EXACT UniProt-feature [] synonym: "AspN" EXACT PSI-MOD-short [] synonym: "isoasparagine" EXACT RESID-alternate [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 4 H 7 N 2 O 3" xref: MassAvg: "131.11" xref: MassMono: "131.045667" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00094 name: L-cysteine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine amide." [PubMed:1892838, PubMed:7149738, RESID:AA0085] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-sulfanylpropanamide" EXACT RESID-systematic [] synonym: "2-amino-3-mercaptopropanamide" EXACT RESID-alternate [] synonym: "amidated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "CysN" EXACT PSI-MOD-short [] synonym: "cysteinamide" EXACT RESID-alternate [] synonym: "Cysteine amide" EXACT UniProt-feature [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1 S 0" xref: DiffMono: "-0.984016" xref: Formula: "C 3 H 7 N 2 O 1 S 1" xref: MassAvg: "119.17" xref: MassMono: "119.027909" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00095 name: L-glutamine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamine residue to L-glutamine amide." [PubMed:7673220, PubMed:9048550, RESID:AA0086] subset: PSI-MOD_slim synonym: "(S)-2-amino-pentanediamide" EXACT RESID-systematic [] synonym: "amidated L-glutamine" EXACT PSI-MOD-alternate [] synonym: "GlnN" EXACT PSI-MOD-short [] synonym: "glutaminamide" EXACT RESID-alternate [] synonym: "Glutamine amide" EXACT UniProt-feature [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 5 H 10 N 3 O 2" xref: MassAvg: "144.15" xref: MassMono: "144.077302" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00907 ! modified L-glutamine residue [Term] id: MOD:00096 name: L-glutamic acid 1-amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamic acid 1-amide." [PubMed:1093875, PubMed:14550575, RESID:AA0087] subset: PSI-MOD_slim synonym: "(S)-2-amino-1-pentanediamic acid" EXACT RESID-systematic [] synonym: "1-amidated L-glutamic acid" EXACT PSI-MOD-alternate [] synonym: "4,5-diamino-5-oxapentanoic acid" EXACT RESID-alternate [] synonym: "GluN" EXACT PSI-MOD-short [] synonym: "Glutamic acid 1-amide" EXACT UniProt-feature [] synonym: "isoglutamine" EXACT RESID-alternate [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 5 H 9 N 2 O 3" xref: MassAvg: "145.14" xref: MassMono: "145.061317" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00097 name: glycine amide namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to glycine amide." [PubMed:13591312, RESID:AA0088] subset: PSI-MOD_slim synonym: "2-aminoacetamide" EXACT RESID-alternate [] synonym: "2-aminoethanamide" EXACT RESID-systematic [] synonym: "amidated glycine" EXACT PSI-MOD-alternate [] synonym: "Glycine amide" EXACT UniProt-feature [] synonym: "GlyN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 2 H 5 N 2 O 1" xref: MassAvg: "73.07" xref: MassMono: "73.040188" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00098 name: L-histidine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to L-histidine amide." [PubMed:2153586, PubMed:2307683, PubMed:2839478, RESID:AA0089] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1H-imidazol-4-yl)propanamide" EXACT RESID-systematic [] synonym: "amidated L-histidine" EXACT PSI-MOD-alternate [] synonym: "HisN" EXACT PSI-MOD-short [] synonym: "histidinamide" EXACT RESID-alternate [] synonym: "Histidine amide" EXACT UniProt-feature [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 6 H 9 N 4 O 1" xref: MassAvg: "153.16" xref: MassMono: "153.077636" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00099 name: L-isoleucine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-isoleucine residue to L-isoleucine amide." [RESID:AA0090] subset: PSI-MOD_slim synonym: "(2S,3S)-2-amino-3-methylpentanamide" EXACT RESID-systematic [] synonym: "amidated L-isoleucine" EXACT PSI-MOD-alternate [] synonym: "IleN" EXACT PSI-MOD-short [] synonym: "isoleucinamide" EXACT RESID-alternate [] synonym: "Isoleucine amide" EXACT UniProt-feature [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 6 H 13 N 2 O 1" xref: MassAvg: "129.18" xref: MassMono: "129.102788" xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00910 ! modified L-isoleucine residue [Term] id: MOD:00100 name: L-leucine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-leucine residue to L-leucine amide." [PubMed:2578459, RESID:AA0091] subset: PSI-MOD_slim synonym: "(S)-2-amino-4-methylpentanamide" EXACT RESID-systematic [] synonym: "amidated L-leucine" EXACT PSI-MOD-alternate [] synonym: "leucinamide" EXACT RESID-alternate [] synonym: "Leucine amide" EXACT UniProt-feature [] synonym: "LeuN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 6 H 13 N 2 O 1" xref: MassAvg: "129.18" xref: MassMono: "129.102788" xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00911 ! modified L-leucine residue [Term] id: MOD:00101 name: L-lysine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to L-lysine amide." [PubMed:6579533, RESID:AA0092] subset: PSI-MOD_slim synonym: "(S)-2,6-diaminohexanamide" EXACT RESID-systematic [] synonym: "amidated L-lysine" EXACT PSI-MOD-alternate [] synonym: "lysinamide" EXACT RESID-alternate [] synonym: "Lysine amide" EXACT UniProt-feature [] synonym: "LysN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 6 H 14 N 3 O 1" xref: MassAvg: "144.19" xref: MassMono: "144.113687" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00102 name: L-methionine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-methionine residue to L-methionine amide." [PubMed:4375977, RESID:AA0093] subset: PSI-MOD_slim synonym: "(S)-2-amino-4-(methylsulfanyl)butanamide" EXACT RESID-systematic [] synonym: "2-amino-4-(methylthio)butanamide" EXACT RESID-alternate [] synonym: "amidated L-methionine" EXACT PSI-MOD-alternate [] synonym: "methioninamide" EXACT RESID-alternate [] synonym: "Methionine amide" EXACT UniProt-feature [] synonym: "MetN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1 S 0" xref: DiffMono: "-0.984016" xref: Formula: "C 5 H 11 N 2 O 1 S 1" xref: MassAvg: "147.22" xref: MassMono: "147.059209" xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00103 name: L-phenylalanine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-phenylalanine residue to L-phenylalanine amide." [PubMed:2905621, PubMed:8868490, RESID:AA0094] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-phenylpropanamide" EXACT RESID-systematic [] synonym: "amidated L-phenylalanine" EXACT PSI-MOD-alternate [] synonym: "PheN" EXACT PSI-MOD-short [] synonym: "phenylalaninamide" EXACT RESID-alternate [] synonym: "Phenylalanine amide" EXACT UniProt-feature [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 9 H 11 N 2 O 1" xref: MassAvg: "163.20" xref: MassMono: "163.087138" xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:00104 name: L-proline amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to L-proline amide." [PubMed:4982117, PubMed:5760861, RESID:AA0095] subset: PSI-MOD_slim synonym: "(S)-pyrrolidine-2-carboxamide" EXACT RESID-systematic [] synonym: "amidated L-proline" EXACT PSI-MOD-alternate [] synonym: "prolinamide" EXACT RESID-alternate [] synonym: "Proline amide" EXACT UniProt-feature [] synonym: "ProN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 5 H 9 N 2 O 1" xref: MassAvg: "113.14" xref: MassMono: "113.071488" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00105 name: L-serine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to L-serine amide." [PubMed:743209, RESID:AA0096] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-hydroxypropanamide" EXACT RESID-systematic [] synonym: "amidated L-serine" EXACT PSI-MOD-alternate [] synonym: "serinamide" EXACT RESID-alternate [] synonym: "Serine amide" EXACT UniProt-feature [] synonym: "SerN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 3 H 7 N 2 O 2" xref: MassAvg: "103.10" xref: MassMono: "103.050752" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00106 name: L-threonine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to L-threonine amide." [PubMed:1390774, RESID:AA0097] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-hydroxybutanamide" EXACT RESID-systematic [] synonym: "amidated L-threonine" EXACT PSI-MOD-alternate [] synonym: "threoninamide" EXACT RESID-alternate [] synonym: "Threonine amide" EXACT UniProt-feature [] synonym: "ThrN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 4 H 9 N 2 O 2" xref: MassAvg: "117.13" xref: MassMono: "117.066403" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00107 name: L-tryptophan amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to L-tryptophan amide." [PubMed:3947348, RESID:AA0098] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1H-indol-3-yl)propanamide" EXACT RESID-systematic [] synonym: "amidated L-tryptophan" EXACT PSI-MOD-alternate [] synonym: "TrpN" EXACT PSI-MOD-short [] synonym: "Tryptophan amide" EXACT UniProt-feature [] synonym: "tryptophanamide" EXACT RESID-alternate [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 11 H 12 N 3 O 1" xref: MassAvg: "202.23" xref: MassMono: "202.098037" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00108 name: L-tyrosine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to L-tyrosine amide." [PubMed:1377792, PubMed:3562898, PubMed:6509012, RESID:AA0099] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(4-hydoxyphenyl)propanamide" EXACT RESID-systematic [] synonym: "amidated L-tyrosine" EXACT PSI-MOD-alternate [] synonym: "TyrN" EXACT PSI-MOD-short [] synonym: "tyrosinamide" EXACT RESID-alternate [] synonym: "Tyrosine amide" EXACT UniProt-feature [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 9 H 11 N 2 O 2" xref: MassAvg: "179.20" xref: MassMono: "179.082053" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00109 name: L-valine amide namespace: PSI-MOD def: "A protein modification that effectively converts an L-valine residue to L-valine amide." [PubMed:2578459, PubMed:5465996, RESID:AA0100] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-methylbutanamide" EXACT RESID-systematic [] synonym: "valinamide" EXACT RESID-alternate [] synonym: "Valine amide " EXACT UniProt-feature [] synonym: "ValN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 5 H 11 N 2 O 1" xref: MassAvg: "115.15" xref: MassMono: "115.087138" xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00883 ! alpha-amidated residue is_a: MOD:00920 ! modified L-valine residue [Term] id: MOD:00110 name: L-cysteine methyl disulfide namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl disulfide." [PubMed:10555576, PubMed:2056535, PubMed:6381494, RESID:AA0101, UniMod:39] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(methyldisulfanediyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(methyldithio)propanoic acid" EXACT RESID-alternate [] synonym: "Beta-methylthiolation" RELATED UniMod-description [] synonym: "Cysteine methyl disulfide" EXACT UniProt-feature [] synonym: "L-3-(methyldithio)alanine" EXACT RESID-alternate [] synonym: "Methylthio" RELATED UniMod-interim [] synonym: "S-methyl thiocysteine" EXACT RESID-alternate [] xref: DiffAvg: "46.09" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 1" xref: DiffMono: "45.987721" xref: Formula: "C 4 H 7 N 1 O 1 S 2" xref: MassAvg: "149.23" xref: MassMono: "148.996906" xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01153 ! methylthiolated residue [Term] id: MOD:00111 name: S-farnesyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-farnesyl-L-cysteine." [DeltaMass:293, PubMed:1409665, PubMed:15609361, PubMed:1872463, PubMed:2684976, RESID:AA0102, UniMod:44] comment: From DeltaMass: (name misspelled "S-farnesyl cystenyl") subset: PSI-MOD_slim synonym: "(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid" EXACT RESID-alternate [] synonym: "Farnesyl" RELATED PSI-MS-label [] synonym: "Farnesylation" RELATED UniMod-description [] synonym: "S-farnesyl cysteine" EXACT UniProt-feature [] synonym: "S-farnesyl Cystenyl" EXACT DeltaMass-label [] synonym: "SFarnCys" EXACT PSI-MOD-short [] xref: DiffAvg: "204.35" xref: DiffFormula: "C 15 H 24 N 0 O 0 S 0" xref: DiffMono: "204.187801" xref: Formula: "C 18 H 29 N 1 O 1 S 1" xref: MassAvg: "307.49" xref: MassMono: "307.196986" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00437 ! farnesylated residue is_a: MOD:01110 ! isoprenylated cysteine [Term] id: MOD:00112 name: S-12-hydroxyfarnesyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-12-hydroxyfarnesyl-L-cysteine." [PubMed:17790543, RESID:AA0103, UniMod:376] subset: PSI-MOD_slim synonym: "(R,E,E,Z)-2-amino-3-(12-hydroxy-3,7,11-trimethyl-3,6,10-dodecatrienylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(12-hydroxy-3,7,11-trimethyl-3,6,10-dodecatrienylthio)propanoic acid" EXACT RESID-alternate [] synonym: "Hydroxyfarnesyl" RELATED PSI-MS-label [] synonym: "hydroxyfarnesyl" RELATED UniMod-description [] synonym: "S-12-hydroxyfarnesyl cysteine" EXACT UniProt-feature [] synonym: "S12HyFarnCys" EXACT PSI-MOD-short [] xref: DiffAvg: "220.35" xref: DiffFormula: "C 15 H 24 N 0 O 1 S 0" xref: DiffMono: "220.182715" xref: Formula: "C 18 H 29 N 1 O 2 S 1" xref: MassAvg: "323.49" xref: MassMono: "323.191900" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01110 ! isoprenylated cysteine [Term] id: MOD:00113 name: S-geranylgeranyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-geranylgeranyl-L-cysteine." [DeltaMass:0, PubMed:1483450, PubMed:15609361, RESID:AA0104, UniMod:48] comment: DeltaMass calculates the mass with two double bonds rather than four subset: PSI-MOD_slim synonym: "(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid" EXACT RESID-alternate [] synonym: "Geranyl-geranyl" RELATED UniMod-description [] synonym: "GeranylGeranyl" RELATED PSI-MS-label [] synonym: "S-geranylgeranyl" EXACT DeltaMass-label [] synonym: "S-geranylgeranyl cysteine" EXACT UniProt-feature [] synonym: "SGergerCys" EXACT PSI-MOD-short [] xref: DiffAvg: "272.47" xref: DiffFormula: "C 20 H 32 N 0 O 0 S 0" xref: DiffMono: "272.250401" xref: Formula: "C 23 H 37 N 1 O 1 S 1" xref: MassAvg: "375.61" xref: MassMono: "375.259586" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00441 ! geranylgeranylated residue is_a: MOD:01110 ! isoprenylated cysteine [Term] id: MOD:00114 name: L-cysteine methyl ester namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine methyl ester." [PubMed:11875433, PubMed:1872463, RESID:AA0105, UniMod:34] comment: Secondary to RESID:AA0102; secondary to RESID:AA0103; secondary to RESID:AA0104. subset: PSI-MOD_slim synonym: "2-amino-3-mercaptopropanoic methyl ester" EXACT RESID-alternate [] synonym: "2-amino-3-sulfanylpropanoic methyl ester" EXACT RESID-alternate [] synonym: "Cysteine methyl ester" EXACT UniProt-feature [] synonym: "mecysteine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "methyl (2R)-2-amino-3-sulfanylpropanoate" EXACT RESID-systematic [] synonym: "methyl esterified L-cysteine" EXACT PSI-MOD-alternate [] synonym: "methyl L-cysteinate" EXACT RESID-alternate [] synonym: "Methylation" RELATED UniMod-description [] synonym: "OMeCys" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 0" xref: DiffMono: "14.015650" xref: Formula: "C 4 H 8 N 1 O 2 S 1" xref: MassAvg: "134.18" xref: MassMono: "134.027574" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00393 ! O-methylated residue is_a: MOD:00599 ! monomethylated residue is_a: MOD:00660 ! methylated cysteine [Term] id: MOD:00115 name: S-palmitoyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-palmitoyl-L-cysteine." [DeltaMass:303, PubMed:1872406, PubMed:3166978, PubMed:8180229, PubMed:8824274, RESID:AA0106, UniMod:47] comment: From DeltaMass: (name misspelled "S-palmityl Cystenyl" and formula incorrect, N and O reversed) Formula: C19H35O1N2S1 Monoisotopic Mass Change: 341.239 Average Mass Change: 341.556 subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(hexadecanoylthio)propanoic acid" EXACT RESID-alternate [] synonym: "cysteine hexadecanoate thioester" EXACT RESID-alternate [] synonym: "cysteine palmitate thioester" EXACT RESID-alternate [] synonym: "Palmitoyl" RELATED PSI-MS-label [] synonym: "Palmitoylation" RELATED UniMod-description [] synonym: "S-palmitoyl cysteine" EXACT UniProt-feature [] synonym: "S-palmitoylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "S-palmityl Cystenyl" EXACT DeltaMass-label [] synonym: "SPamCys" EXACT PSI-MOD-short [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1 S 0" xref: DiffMono: "238.229666" xref: Formula: "C 19 H 35 N 1 O 2 S 1" xref: MassAvg: "341.55" xref: MassMono: "341.238850" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00653 ! S-palmitoylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00116 name: S-diacylglycerol-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-diacylglycerol-L-cysteine." [PubMed:10896212, PubMed:4575979, PubMed:9056182, RESID:AA0107, UniMod:377] comment: Incidental to RESID:AA0060. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2-((Z)-9-octadecenoyloxy)-3-(hexadecanoyloxy)propyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-[(S)-2-((Z)-9-octadecenoyloxy)-3-(hexadecanoyloxy)propyl]thiopropanoic acid" EXACT RESID-alternate [] synonym: "Diacylglycerol" RELATED PSI-MS-label [] synonym: "diacylglycerol" RELATED UniMod-description [] synonym: "S-(1-2'-oleoyl-3'-palmitoyl-glycerol)cysteine" EXACT RESID-alternate [] synonym: "S-(2',3'-diacylglycerol)-L-cysteine" EXACT PSI-MOD-alternate [] synonym: "S-diacylglycerol cysteine" EXACT UniProt-feature [] xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00117 name: S-(L-isoglutamyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and an L-glutamine residue by a thioester bond to form S-(L-isoglutamyl)-L-cysteine." [ChEBI:22021, DeltaMass:0, PubMed:6838833, RESID:AA0108] comment: Cross-link 2; DeltaMass calculates the mass difference from glutamic acid rather than glutamine. subset: PSI-MOD_slim synonym: "(S)-2-amino-5-((R)-2-amino-2-carboxyethyl)sulfanyl-5-oxopentanoic acid" EXACT RESID-systematic [] synonym: "(S,R)-2-amino-4-[S-(2-amino-2-carboxyethyl)thiocarboxy]butanoic acid" EXACT RESID-alternate [] synonym: "2-amino-5-(2-amino-2-carboxyethyl)thio-5-oxopentanoic acid" EXACT RESID-alternate [] synonym: "gamma-(S-cysteinyl)glutamic acid" EXACT RESID-alternate [] synonym: "Isoglutamyl cysteine thioester (Cys-Gln)" EXACT UniProt-feature [] synonym: "S-gamma-glutamyl (crosslinked to cysteine)" EXACT DeltaMass-label [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0 S 0" xref: DiffMono: "-17.026549" xref: Formula: "C 8 H 10 N 2 O 3 S 1" xref: MassAvg: "214.24" xref: MassMono: "214.041213" xref: Origin: "C, Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00907 ! modified L-glutamine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] id: MOD:00118 name: 2'-(S-L-cysteinyl)-L-histidine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-histidine residue by a thioether bond to form 2'-(S-L-cysteinyl)-L-histidine." [DeltaMass:0, PubMed:6210696, RESID:AA0109] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[2-((R)-2-amino-2-carboxyethyl)sulfanylimidazol-4-yl]propanoic acid" EXACT RESID-systematic [] synonym: "2'-(S-cysteinyl)-histidine (Cys-His)" EXACT UniProt-feature [] synonym: "S-(2'-histidyl)cysteine" EXACT RESID-alternate [] synonym: "S-(2-histidyl)- (crosslinked to cysteine)" EXACT DeltaMass-label [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 9 H 10 N 4 O 2 S 1" xref: MassAvg: "238.27" xref: MassMono: "238.052447" xref: Origin: "C, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00119 name: L-lanthionine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-serine residue by a thioether bond to form L-lanthionine." [ChEBI:21347, DeltaMass:7, RESID:AA0110] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-S-(2-amino-2-carboxyethyl)-L-cysteine" EXACT RESID-alternate [] synonym: "(R,R)-2,6-diamino-4-thiaheptanedioic acid" EXACT RESID-alternate [] synonym: "(R,R)-3,3'-thiobis-(2-aminopropanoic acid)" EXACT RESID-alternate [] synonym: "(R,R)-bis(2-amino-2-carboxyethyl)sulfanediyl" EXACT RESID-systematic [] synonym: "(R,R)-bis(2-amino-2-carboxyethyl)sulfide" EXACT RESID-alternate [] synonym: "2-amino-3-(2-amino-2-carboxyethyl)sulfanylpropanoic acid" EXACT RESID-alternate [] synonym: "3,3'-thiobis-L-alanine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 6 H 8 N 2 O 2 S 1" xref: MassAvg: "172.20" xref: MassMono: "172.030649" xref: Origin: "C, S" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00916 ! modified L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00120 name: meso-lanthionine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-serine residue by a thioether bond to form meso-lanthionine." [PubMed:15023056, PubMed:3769923, RESID:AA0111] comment: Cross-link 2. This modification has not been observed to occur naturally. subset: PSI-MOD_slim synonym: "(R)-S-(2-amino-2-carboxyethyl)-D-cysteine" EXACT RESID-alternate [] synonym: "(R,S)-2,6-diamino-4-thiaheptanedioic acid" EXACT RESID-alternate [] synonym: "(R,S)-3,3'-thiobis-(2-aminopropanoic acid)" EXACT RESID-alternate [] synonym: "(R,S)-bis(2-amino-2-carboxyethyl)sulfanediyl" EXACT RESID-systematic [] synonym: "(R,S)-bis(2-amino-2-carboxyethyl)sulfide" EXACT RESID-alternate [] synonym: "3,3'-thiobis-meso-alanine" EXACT RESID-alternate [] synonym: "cysteine-3-D-alanine thioether" EXACT RESID-alternate [] synonym: "Lanthionine (Ser-Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 6 H 8 N 2 O 2 S 1" xref: MassAvg: "172.20" xref: MassMono: "172.030649" xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00916 ! modified L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00121 name: 3-methyl-L-lanthionine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-threonine residue by a thioether bond to form 3-methyl-L-lanthionine." [PubMed:3769923, RESID:AA0112] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S,3S,2'R)-2-amino-3-[(2-amino-2-carboxyethyl)sulfanyl]butanoic acid" EXACT RESID-systematic [] synonym: "(2S,3S,2'R)-2-amino-3-[(2-amino-2-carboxyethyl)thio]butanoic acid" EXACT RESID-alternate [] synonym: "(2S,3S,6R)-2,6-diamino-3-methyl-4-thiaheptanedioic acid" EXACT RESID-alternate [] synonym: "(2S-[2R*,3R*(S*)])-2-amino-3-[(2-amino-2-carboxyethyl)thio]butanoic acid" EXACT RESID-alternate [] synonym: "Beta-methyllanthionine (Thr-Cys)" EXACT UniProt-feature [] synonym: "cysteine-3-D-butyrine thioether" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 7 H 10 N 2 O 2 S 1" xref: MassAvg: "186.23" xref: MassMono: "186.046299" xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00122 name: 3'-(S-L-cysteinyl)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-tyrosine residue by a thioether bond to form 2-(S-L-cysteinyl)-L-tyrosine." [DeltaMass:0, PubMed:15917234, PubMed:2002850, RESID:AA0113] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S,R)-2-amino-3-[3-(2-amino-2-carboxyethylsulfanyl)-4-hydroxyphenyl]propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-[3-(2-amino-2-carboxyethylthio)-4-hydroxyphenyl]propanoic acid" EXACT RESID-alternate [] synonym: "3'-(S-cysteinyl)-tyrosine (Tyr-Cys)" EXACT UniProt-feature [] synonym: "S-(3'-tyrosinyl)cysteine" EXACT RESID-alternate [] synonym: "S-(3-Tyr) (Crosslinked to Cysteine)" EXACT DeltaMass-label [] synonym: "XLNKSCys3'Tyr" EXACT PSI-MOD-short [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 12 H 12 N 2 O 3 S 1" xref: MassAvg: "264.30" xref: MassMono: "264.056863" xref: Origin: "C, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00123 name: N6-carboxy-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-carboxy-L-lysine." [PubMed:11369851, PubMed:4436319, PubMed:637859, PubMed:7754395, RESID:AA0114, UniMod:299] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-(carboxyamino)hexanoic acid" EXACT RESID-systematic [] synonym: "2-amino-6-carbamic hexanoic acid" EXACT RESID-alternate [] synonym: "Carboxy" RELATED UniMod-interim [] synonym: "Carboxylation" RELATED UniMod-description [] synonym: "lysine NZ-carboxylic acid" EXACT RESID-alternate [] synonym: "N6-carbamyllysine [misnomer]" RELATED RESID-misnomer [] synonym: "N6-carboxylysine" EXACT UniProt-feature [] synonym: "N6-carboxylysine" EXACT RESID-alternate [] synonym: "N6CbxLys" EXACT PSI-MOD-short [] xref: DiffAvg: "44.01" xref: DiffFormula: "C 1 H 0 N 0 O 2" xref: DiffMono: "43.989829" xref: Formula: "C 7 H 12 N 2 O 3" xref: MassAvg: "172.18" xref: MassMono: "172.084792" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01152 ! carboxylated residue [Term] id: MOD:00124 name: N6-1-carboxyethyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-1-carboxyethyl-L-lysine." [PubMed:3123486, PubMed:8253186, PubMed:8421682, RESID:AA0115, UniMod:378] subset: PSI-MOD_slim synonym: "(S,S)-2-amino-6-(1-carboxyethyl)aminohexanoic acid" EXACT RESID-systematic [] synonym: "Carboxyethyl" RELATED PSI-MS-label [] synonym: "carboxyethyl" RELATED UniMod-description [] synonym: "N6-(1-carboxyethyl)lysine" EXACT RESID-alternate [] synonym: "N6-1-carboxyethyl lysine" EXACT UniProt-feature [] synonym: "NZ-(1-carboxyethyl)lysine" EXACT RESID-alternate [] xref: DiffAvg: "72.06" xref: DiffFormula: "C 3 H 4 N 0 O 2" xref: DiffMono: "72.021129" xref: Formula: "C 9 H 16 N 2 O 3" xref: MassAvg: "200.23" xref: MassMono: "200.116092" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00125 name: Hypusine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to hypusine, N6-(4-amino-2-hydroxybutyl)-L-lysine." [DeltaMass:0, PubMed:6806267, PubMed:8108861, RESID:AA0116, UniMod:379] subset: PSI-MOD_slim synonym: "(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "Hypu" EXACT PSI-MOD-short [] synonym: "Hypusine" EXACT UniProt-feature [] synonym: "hypusine" EXACT RESID-alternate [] synonym: "Hypusine" RELATED PSI-MS-label [] synonym: "hypusine" RELATED UniMod-description [] synonym: "N-(4-NH2-2-OH-butyl)- (of Lysine)" EXACT DeltaMass-label [] xref: DiffAvg: "87.12" xref: DiffFormula: "C 4 H 9 N 1 O 1" xref: DiffMono: "87.068414" xref: Formula: "C 10 H 21 N 3 O 2" xref: MassAvg: "215.29" xref: MassMono: "215.163377" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00126 name: N6-biotinyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-biotinyl-L-lysine." [DeltaMass:305, PubMed:16109483, PubMed:3178228, PubMed:7948875, PubMed:8747466, RESID:AA0117, UniMod:3] comment: From DeltaMass: Average Mass: 354 Formula:C 16 H 26 O 4 N 3 S 1 (formula incorrect, N and O reversed) Monoisotopic Mass Change:354.172 Average Mass Change:354.471 References:PE Sciex. subset: PSI-MOD_slim synonym: "(3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine" EXACT RESID-alternate [] synonym: "(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid" EXACT RESID-systematic [] synonym: "biocytin" EXACT RESID-alternate [] synonym: "Biotin" RELATED PSI-MS-label [] synonym: "Biotin (covalent)" EXACT UniProt-feature [] synonym: "biotinyl lysyl" EXACT DeltaMass-label [] synonym: "Biotinylation" RELATED UniMod-description [] synonym: "epsilon-N-biotinyllysine" EXACT RESID-alternate [] synonym: "N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine" EXACT RESID-alternate [] synonym: "N6-biotinyllysine" EXACT RESID-alternate [] xref: DiffAvg: "226.30" xref: DiffFormula: "C 10 H 14 N 2 O 2 S 1" xref: DiffMono: "226.077599" xref: Formula: "C 16 H 26 N 4 O 3 S 1" xref: MassAvg: "354.47" xref: MassMono: "354.172562" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00127 name: N6-lipoyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-lipoyl-L-lysine." [DeltaMass:0, PubMed:3421911, PubMed:3522581, PubMed:7719855, RESID:AA0118, UniMod:42] comment: From DeltaMass: Average Mass: 188. subset: PSI-MOD_slim synonym: "(2S,6'R)-2-amino-6-(6,8-dithiooctanamido)hexanoic acid" EXACT RESID-alternate [] synonym: "(S)-2-amino-6-[5-((R)-1,2-dithiolan-3-yl)pentanamido]hexanoic acid" EXACT RESID-systematic [] synonym: "2-amino-6-(5-[1,2-dithiolan-3-yl]-1-oxopentyl)aminohexanoic acid" EXACT RESID-alternate [] synonym: "Lipoyl" RELATED PSI-MS-label [] synonym: "Lipoyl" RELATED UniMod-description [] synonym: "Lipoyl (covalent)" EXACT UniProt-feature [] synonym: "N-Lipoyl- (on Lysine)" EXACT DeltaMass-label [] synonym: "N6-6,8-dithiooctanoyllysine" EXACT RESID-alternate [] synonym: "N6-lipoyllysine" EXACT RESID-alternate [] xref: DiffAvg: "188.31" xref: DiffFormula: "C 8 H 12 N 0 O 1 S 2" xref: DiffMono: "188.032957" xref: Formula: "C 14 H 24 N 2 O 2 S 2" xref: MassAvg: "316.48" xref: MassMono: "316.127920" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00128 name: N6-pyridoxal phosphate-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-pyridoxal phosphate-L-lysine." [DeltaMass:0, PubMed:1544460, RESID:AA0119, UniMod:46] comment: From DeltaMass: Average Mass: 231 subset: PSI-MOD_slim synonym: "(S)-2-amino-6-[(3-hydroxy-2-methyl-5-phosphonooxymethyl-4-pyridine)methyleneamino]hexanoic acid" EXACT RESID-systematic [] synonym: "Pyridoxal phosphate" RELATED UniMod-description [] synonym: "Pyridoxal phosphate (covalent)" EXACT UniProt-feature [] synonym: "Pyridoxal phosphate (Schiff Base formed to lysine)" EXACT DeltaMass-label [] synonym: "PyridoxalPhosphate" RELATED PSI-MS-label [] xref: DiffAvg: "229.13" xref: DiffFormula: "C 8 H 8 N 1 O 5 P 1" xref: DiffMono: "229.014009" xref: Formula: "C 14 H 20 N 3 O 6 P 1" xref: MassAvg: "357.30" xref: MassMono: "357.108972" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00129 name: N6-retinylidene-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-retinylidene-L-lysine, the adduct of retinal." [PubMed:6794028, PubMed:6870827, RESID:AA0120, UniMod:380] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid" EXACT RESID-systematic [] synonym: "N6-retinal-L-lysine" EXACT RESID-alternate [] synonym: "N6-retinyl-lysine" EXACT RESID-alternate [] synonym: "retinal" RELATED UniMod-description [] synonym: "Retinal chromophore (covalent)" EXACT UniProt-feature [] synonym: "Retinylidene" RELATED PSI-MS-label [] xref: DiffAvg: "266.42" xref: DiffFormula: "C 20 H 26 N 0 O 0" xref: DiffMono: "266.203451" xref: Formula: "C 26 H 38 N 2 O 1" xref: MassAvg: "394.59" xref: MassMono: "394.298414" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00130 name: L-allysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to L-allysine." [ChEBI:17917, DeltaMass:0, PubMed:11120890, PubMed:11332453, PubMed:358196, PubMed:5337886, PubMed:5529814, RESID:AA0121, UniMod:352] comment: From DeltaMass: Average Mass: -1 subset: PSI-MOD_slim synonym: "(S)-2-amino-6-oxohexanoic acid" EXACT RESID-systematic [] synonym: "2-amino-5-formylvaleric acid" EXACT RESID-alternate [] synonym: "2-amino-adipic acid semialdahyde" EXACT RESID-alternate [] synonym: "2-aminoadipate 6-semialdehyde" EXACT RESID-alternate [] synonym: "5-formyl-norvaline" EXACT RESID-alternate [] synonym: "6-oxonorleucine" EXACT RESID-alternate [] synonym: "Allysine" EXACT UniProt-feature [] synonym: "Allysine (from Lysine)" EXACT DeltaMass-label [] synonym: "alpha-amino-adipic acid delta-semialdahyde" EXACT RESID-alternate [] synonym: "Lys->Allysine" RELATED PSI-MS-label [] synonym: "Lysine oxidation to aminoadipic semialdehyde" RELATED UniMod-description [] synonym: "Oxidation of lysine (to aminoadipic semialdehyde)" EXACT DeltaMass-label [] xref: DiffAvg: "-1.03" xref: DiffFormula: "C 0 H -3 N -1 O 1" xref: DiffMono: "-1.031634" xref: Formula: "C 6 H 9 N 1 O 2" xref: MassAvg: "127.14" xref: MassMono: "127.063329" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00131 name: L-2-aminoadipic acid namespace: PSI-MOD def: "modification from RESID" [DeltaMass:353, PubMed:336041, PubMed:358196, PubMed:7419498, RESID:AA0122, UniMod:381] comment: From DeltaMass: Average Mass: 15 Monoisotopic Mass Change:14.97 Average Mass Change:15 References:Amici A, Levine, RL, Tsai, L, and Stadtman, ER: Conversion of amino acid residues in proteins and amino acid homopolymers to carbonyl derivatives by metal-catalyzed oxidation reactions. Journal of Biological Chemistry 264: 3341-3346 1989.Requena JR, Chao CC, Levine RL, and Stadtman ER: Glutamic and aminoadipic semialdehydes are the main carbonyl products of metal-catalyzed oxidation of proteins. Proceedings of the National Academy of Sciences USA 98: 69-74 2001. Notes:Expected reaction following oxidation of lysine to aminoadipic semialdehyde. Not proven experimentally but deduced by reference to the similar known reaction of oxidation of Arg to Glu via the semialdehyde. subset: PSI-MOD_slim synonym: "(S)-2-aminohexanedioic acid" EXACT RESID-systematic [] synonym: "2-amino-1,4-butanedicarboxylic acid" EXACT RESID-alternate [] synonym: "alpha-amino adipic acid" RELATED UniMod-description [] synonym: "L-alpha-aminoadipic acid" EXACT RESID-alternate [] synonym: "Lys->AminoadipicAcid" RELATED PSI-MS-label [] synonym: "Oxidation of lysine (to aminoadipic acid)" EXACT DeltaMass-label [] xref: DiffAvg: "14.97" xref: DiffFormula: "C 0 H -3 N -1 O 2" xref: DiffMono: "14.963280" xref: Formula: "C 6 H 9 N 1 O 3" xref: MassAvg: "143.14" xref: MassMono: "143.058243" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00132 name: L-lysinoalanine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-serine residue and an L-lysine residue to release water and form 2-amino-6-(2-amino-2-carboxyethylamino)hexanoic acid." [DeltaMass:0, PubMed:2544544, RESID:AA0123] comment: Cross-link 2 From DeltaMass: Average Mass: -34. subset: PSI-MOD_slim synonym: "(2S)-2-amino-6-((2Xi)-2-amino-2-carboxyethylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "(2Xi,9S)-lysinoalanine" EXACT RESID-alternate [] synonym: "Lysinoalanine (from Cysteine)" EXACT DeltaMass-label [] synonym: "Lysinoalanine (Ser-Lys)" EXACT UniProt-feature [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 9 H 15 N 3 O 2" xref: MassAvg: "197.23" xref: MassMono: "197.116427" xref: Origin: "K, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00916 ! modified L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00133 name: N6-(L-isoglutamyl)-L-lysine (Gln) namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-glutamine residue and an L-lysine residue by an isopeptide bond to form N6-(L-isoglutamyl)-L-lysine." [ChEBI:21863, DeltaMass:0, PubMed:2461365, PubMed:5637041, PubMed:5656070, PubMed:8598899, RESID:AA0124] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S,S)-2-amino-6-[(4-amino-4-carboxybutanoyl)amino]hexanoic acid" EXACT RESID-systematic [] synonym: "gamma-(N6-lysyl)glutamic acid" EXACT RESID-alternate [] synonym: "Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-...)" EXACT UniProt-feature [] synonym: "N alpha -(gamma-Glutamyl)-lysine" EXACT DeltaMass-label [] synonym: "N(epsilon)-(gamma-glutamyl)lysine" EXACT RESID-alternate [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" xref: DiffMono: "-17.026549" xref: Formula: "C 11 H 17 N 3 O 3" xref: MassAvg: "239.27" xref: MassMono: "239.126991" xref: Origin: "K, Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00688 ! isopeptide crosslinked residues is_a: MOD:00907 ! modified L-glutamine residue is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] id: MOD:00134 name: N6-glycyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-lysine residue and a glycine residue by an isopeptide bond to form N6-glycyl-L-lysine." [ChEBI:21885, RESID:AA0125] comment: Cross-link 2; this is the common crosslink structure formed by ubiquitin, SUMO, and similar proteins. subset: PSI-MOD_slim synonym: "(S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid" EXACT RESID-systematic [] synonym: "Glycyl lysine isopeptide (Lys-Gly) (interchain with G-...)" EXACT UniProt-feature [] synonym: "N6-glycyllysine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 8 H 14 N 3 O 2" xref: MassAvg: "184.22" xref: MassMono: "184.108602" xref: Origin: "G, K" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00688 ! isopeptide crosslinked residues is_a: MOD:00908 ! modified glycine residue is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00135 name: N-(L-isoaspartyl)glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-aspartic acid residue and a glycine residue by an isopeptide bond to form N-(L-isoaspartyl)glycine." [ChEBI:21479, PubMed:1826288, RESID:AA0126] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S)-2-amino-4-(carboxymethyl)amino-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "2-amino-N4-(carboxymethyl)-butanediamic acid" EXACT RESID-alternate [] synonym: "isoaspartyl glycine" EXACT RESID-alternate [] synonym: "Isoaspartyl glycine isopeptide (Gly-Asn)" EXACT UniProt-feature [] synonym: "N-beta-aspartylglycine" EXACT RESID-alternate [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" xref: DiffMono: "-17.026549" xref: Formula: "C 6 H 7 N 2 O 3" xref: MassAvg: "155.13" xref: MassMono: "155.045667" xref: Origin: "G, N" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00688 ! isopeptide crosslinked residues is_a: MOD:00903 ! modified L-asparagine residue is_a: MOD:00908 ! modified glycine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] id: MOD:00136 name: pyruvic acid (Cys) namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to pyruvic acid." [PubMed:10085076, PubMed:3042771, PubMed:8464063, RESID:AA0127, UniMod:382] subset: PSI-MOD_slim synonym: "Pyruvic acid (Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-33.10" xref: DiffFormula: "C 0 H -3 N -1 O 1 S -1" xref: DiffMono: "-33.003705" xref: Formula: "C 3 H 3 O 2" xref: MassAvg: "71.05" xref: MassMono: "71.013304" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01154 ! pyruvic acid [Term] id: MOD:00137 name: L-3-phenyllactic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-phenylalanine residue into L-3-phenyllactic acid." [PubMed:1973541, RESID:AA0128, UniMod:7] comment: This modification is not the result of deamidation, instead the alpha amino group is replaced with an hydroxyl group. subset: PSI-MOD_slim synonym: "(S)-2-hydroxy-3-phenylpropanoic acid" EXACT RESID-systematic [] synonym: "3-phenyllactic acid" EXACT UniProt-feature [] synonym: "Deamidated" RELATED UniMod-interim [] synonym: "Deamidation" RELATED UniMod-description [] xref: DiffAvg: "0.98" xref: DiffFormula: "C 0 H -1 N -1 O 1" xref: DiffMono: "0.984016" xref: Formula: "C 9 H 9 O 2" xref: MassAvg: "149.17" xref: MassMono: "149.060255" xref: Origin: "F" xref: TermSpec: "N-term" is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:00138 name: 2-oxobutanoic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue into 2-oxobutanoic acid." [PubMed:15023056, PubMed:1680314, PubMed:2253617, PubMed:2764678, RESID:AA0129, UniMod:385] subset: PSI-MOD_slim synonym: "2-oxobutanoic acid" EXACT UniProt-feature [] synonym: "2-oxobutanoic acid" EXACT RESID-systematic [] synonym: "Ammonia-loss" RELATED UniMod-interim [] synonym: "Loss of ammonia" RELATED UniMod-description [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" xref: DiffMono: "-17.026549" xref: Formula: "C 4 H 5 O 2" xref: MassAvg: "85.08" xref: MassMono: "85.028954" xref: Origin: "T" xref: TermSpec: "N-term" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01160 ! deaminated residue [Term] id: MOD:00139 name: N2-succinyl-L-tryptophan namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to N2-succinyl-L-tryptophan." [PubMed:11857757, PubMed:12175151, PubMed:8471040, RESID:AA0130, UniMod:64] subset: PSI-MOD_slim synonym: "(S)-2-(3-carboxypropanoyl)amino-3-(1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "N2-succinyltryptophan" EXACT UniProt-feature [] synonym: "Succinic anhydride labeling reagent light form (N-term & K)" RELATED UniMod-description [] synonym: "Succinyl" RELATED PSI-MS-label [] xref: DiffAvg: "100.07" xref: DiffFormula: "C 4 H 4 N 0 O 3" xref: DiffMono: "100.016044" xref: Formula: "C 15 H 15 N 2 O 4" xref: MassAvg: "287.29" xref: MassMono: "287.103182" xref: Origin: "W" xref: TermSpec: "N-term" is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00140 name: S-phycocyanobilin-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycocyanobilin." [ChEBI:15617, DeltaMass:0, PubMed:16644722, PubMed:3208761, PubMed:3838747, PubMed:7918400, RESID:AA0131, UniMod:387] comment: From DeltaMass: Average Mass: 587. subset: PSI-MOD_slim synonym: "(2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-18-ethyl-1,2,3,19,21,22,24-heptahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "(2R,3R)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-2,7,13,17-tetramethyl-1,2,3,19,21,22,24-heptahydrobilin-1,19(21H,22H,24H)-dione" EXACT RESID-systematic [] synonym: "phycobilin cysteine" EXACT RESID-alternate [] synonym: "Phycocyanobilin" RELATED PSI-MS-label [] synonym: "phycocyanobilin" RELATED UniMod-description [] synonym: "phycocyanobilin cysteine adduct" EXACT RESID-alternate [] synonym: "S-Phycocyanobilin (on Cysteine)" EXACT DeltaMass-label [] xref: DiffAvg: "586.68" xref: DiffFormula: "C 33 H 38 N 4 O 6 S 0" xref: DiffMono: "586.279135" xref: Formula: "C 36 H 43 N 5 O 7 S 1" xref: MassAvg: "689.82" xref: MassMono: "689.288320" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00141 name: S-phycoerythrobilin-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycoerythrobilin." [ChEBI:15618, PubMed:14588022, PubMed:3208761, PubMed:3838747, PubMed:8876649, RESID:AA0132, UniMod:388] subset: PSI-MOD_slim synonym: "(2S,3R,16R)-18-ethenyl-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-2,3,15,16-tetrahydrobilin-1,19(21H,22H,24H)-dione" EXACT RESID-systematic [] synonym: "18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,3,15,16-tetrahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "Phycoerythrobilin" RELATED PSI-MS-label [] synonym: "phycoerythrobilin" RELATED UniMod-description [] synonym: "phycoerythrobilin cysteine adduct" EXACT RESID-alternate [] xref: DiffAvg: "588.69" xref: DiffFormula: "C 33 H 40 N 4 O 6 S 0" xref: DiffMono: "588.294785" xref: Formula: "C 36 H 45 N 5 O 7 S 1" xref: MassAvg: "691.84" xref: MassMono: "691.303970" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00142 name: S-phytochromobilin-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phytochromobilin." [ChEBI:15619, PubMed:1634523, PubMed:16593380, PubMed:3208761, PubMed:7918400, RESID:AA0133, UniMod:389] subset: PSI-MOD_slim synonym: "18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-1,2,3,19,22,24-hexahydro-2,7,13,17-tetramethyl-1,19-dioxo-21H-biline-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "18-ethenyl-3-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-2,3-dihydro-(21H,24H)-biline-1,19-dione" EXACT RESID-systematic [] synonym: "phytochrome chromophore" EXACT RESID-alternate [] synonym: "Phytochromobilin" RELATED PSI-MS-label [] synonym: "phytochromobilin" RELATED UniMod-description [] synonym: "phytochromobilin cysteine adduct" EXACT RESID-alternate [] xref: DiffAvg: "584.66" xref: DiffFormula: "C 33 H 36 N 4 O 6 S 0" xref: DiffMono: "584.263485" xref: Formula: "C 36 H 41 N 5 O 7 S 1" xref: MassAvg: "687.81" xref: MassMono: "687.272670" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00143 name: heme-bis-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between two cysteine residues and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [ChEBI:17627, PubMed:5545094, PubMed:8827449, RESID:AA0134] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "2,4-bis[1-(S-cysteinyl)ethyl]protoporphyrin IX" EXACT RESID-alternate [] synonym: "[7,12-bis((S)-1-[((R)-2-amino-2-carboxy)ethylsulfanyl]ethyl)-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "biscysteinyl heme" EXACT RESID-alternate [] synonym: "Heme (covalent)" EXACT UniProt-feature [] xref: DiffAvg: "616.49" xref: DiffFormula: "C 34 Fe 1 H 32 N 4 O 4 S 0" xref: DiffMono: "616.177293" xref: Formula: "C 40 Fe 1 H 42 N 6 O 6 S 2" xref: MassAvg: "822.77" xref: MassMono: "822.195663" xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00144 name: heme-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [ChEBI:17627, DeltaMass:0, PubMed:170910, PubMed:192772, PubMed:2536325, PubMed:9535866, RESID:AA0135, UniMod:390] comment: From DeltaMass: Average Mass: 617. subset: PSI-MOD_slim synonym: "4-[1-(S-cysteinyl)ethyl]protoporphyrin IX" EXACT RESID-alternate [] synonym: "[12-ethenyl-7-((S)-1-[(R)-2-amino-2-carboxy]ethylsulfanyl)ethyl-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "cysteinyl heme" EXACT RESID-alternate [] synonym: "Heme" RELATED PSI-MS-label [] synonym: "heme" RELATED UniMod-description [] synonym: "Heme (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "S-Heme (on Cysteine)" EXACT DeltaMass-label [] xref: DiffAvg: "616.49" xref: DiffFormula: "C 34 Fe 1 H 32 N 4 O 4 S 0" xref: DiffMono: "616.177293" xref: Formula: "C 37 Fe 1 H 37 N 5 O 5 S 1" xref: MassAvg: "719.63" xref: MassMono: "719.186478" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00145 name: tetrakis-L-cysteinyl iron namespace: PSI-MOD def: "modification from RESID" [PubMed:1303768, PubMed:2244884, RESID:AA0136] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "tetrakis(cysteinato)-1kappaS,2kappaS,3kappaS,4kappaS-iron" EXACT RESID-systematic [] xref: DiffAvg: "51.81" xref: DiffFormula: "C 0 Fe 1 H -4 N 0 O 0 S 0" xref: DiffMono: "51.903637" xref: Formula: "C 12 Fe 1 H 16 N 4 O 4 S 4" xref: MassAvg: "464.38" xref: MassMono: "463.940376" xref: Origin: "C, C, C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00738 ! iron containing modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00146 name: tetrakis-L-cysteinyl diiron disulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:2123937, PubMed:6801028, PubMed:7763242, PubMed:8688437, RESID:AA0137] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "di-mu-sulfidobis[bis(cysteinato)-kappaS,KappaS-iron]" EXACT RESID-alternate [] synonym: "tetrakis(cysteinato)-1kappaS,1kappaS,2kappaS,2kappaS-di-mu-sulfidodiiron" EXACT RESID-systematic [] xref: DiffAvg: "171.79" xref: DiffFormula: "C 0 Fe 2 H -4 N 0 O 0 S 2" xref: DiffMono: "171.782717" xref: Formula: "C 12 Fe 2 H 16 N 4 O 4 S 6" xref: MassAvg: "584.36" xref: MassMono: "583.819456" xref: Origin: "C, C, C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00147 name: hexakis-L-cysteinyl triiron trisulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:3379067, PubMed:3932661, PubMed:7354058, RESID:AA0138] comment: Cross-link 6. subset: PSI-MOD_slim synonym: "tri-mu-sulfidotris(biscysteinato-kappaS-iron)" EXACT RESID-systematic [] xref: DiffAvg: "257.68" xref: DiffFormula: "C 0 Fe 3 H -6 N 0 O 0 S 3" xref: DiffMono: "257.674075" xref: Formula: "C 18 Fe 3 H 24 N 6 O 6 S 9" xref: MassAvg: "876.54" xref: MassMono: "875.729184" xref: Origin: "C, C, C, C, C, C" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00148 name: tris-L-cysteinyl triiron tetrasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:10555576, PubMed:2056535, PubMed:3422475, PubMed:6848518, PubMed:7819255, PubMed:9063899, RESID:AA0139] comment: Cross-link 3. subset: PSI-MOD_slim synonym: "mu3-sulfido tri-mu-sulfido tris-S-L-cysteinyl triiron" EXACT RESID-alternate [] synonym: "mu3-sulfido-tri-mu-sulfidotris(cysteinato-kappaS-iron)" EXACT RESID-systematic [] synonym: "tris-L-cysteinyl triiron tetrasulfide C3 cluster" EXACT RESID-alternate [] synonym: "tris-L-cysteinyl triiron tetrasulfide cubane form" EXACT RESID-alternate [] synonym: "tris-L-cysteinyl triiron tetrasulfide cuboid cluster" EXACT RESID-alternate [] synonym: "tris-L-cysteinyl triiron tetrasulfide trigonal cluster" EXACT RESID-alternate [] xref: DiffAvg: "292.77" xref: DiffFormula: "C 0 Fe 3 H -3 N 0 O 0 S 4" xref: DiffMono: "292.669621" xref: Formula: "C 9 Fe 3 H 12 N 3 O 3 S 7" xref: MassAvg: "602.20" xref: MassMono: "601.697176" xref: Origin: "C, C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00149 name: tetrakis-L-cysteinyl tetrairon tetrasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:3351918, PubMed:7803404, PubMed:7819196, PubMed:932007, RESID:AA0140] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "tetra-mu3-sulfidotetrakis(S-cysteinyliron)" EXACT RESID-alternate [] synonym: "tetrakis(cysteinato)-1kappaS,2kappaS,3kappaS,4kappaS-tetra-mu3-sulfido-tetrahedro-tetrairon" EXACT RESID-systematic [] xref: DiffAvg: "347.61" xref: DiffFormula: "C 0 Fe 4 H -4 N 0 O 0 S 4" xref: DiffMono: "347.596734" xref: Formula: "C 12 Fe 4 H 16 N 4 O 4 S 8" xref: MassAvg: "760.18" xref: MassMono: "759.633473" xref: Origin: "C, C, C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00150 name: L-cysteinyl-L-histidino-homocitryl molybdenum heptairon nonasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:10525412, PubMed:12215645, PubMed:12733878, PubMed:1529354, PubMed:8027059, RESID:AA0141] comment: Cross-link 2; incidental to RESID:AA0300. subset: PSI-MOD_slim synonym: "nitrogenase iron-molybdenum cofactor" EXACT RESID-alternate [] xref: DiffAvg: "991.59" xref: DiffFormula: "C 7 Fe 7 H 6 Mo 1 N 1 O 7 S 9" xref: DiffMono: "993.213036" xref: Formula: "C 16 Fe 7 H 18 Mo 1 N 5 O 9 S 10" xref: MassAvg: "1231.87" xref: MassMono: "1233.281133" xref: Origin: "C, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00743 ! molybdenum containing modified residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00151 name: L-cysteinyl molybdopterin namespace: PSI-MOD def: "modification from UniMod and Resid" [PubMed:14527393, PubMed:7878465, PubMed:9428520, RESID:AA0142, UniMod:391] subset: PSI-MOD_slim synonym: "8-amino-2-(2-amino-2-carboxyethyl)sulfanyl-4,5a,6,9,10,11,11a-heptahydro-4-(phosphoric acid)methyl-2,2,10-trioxo-pteridino[6,7-5,6]pyrano[3,4-4,3][1,2,5]molybdadithiolene" EXACT RESID-systematic [] synonym: "cysteinyl Mo-pterin" EXACT RESID-alternate [] synonym: "molybdoenzyme molybdenum cofactor" EXACT RESID-alternate [] synonym: "Molybdopterin" RELATED PSI-MS-label [] synonym: "molybdopterin" RELATED UniMod-description [] xref: DiffAvg: "520.29" xref: DiffFormula: "C 10 H 11 Mo 1 N 5 O 8 P 1 S 2" xref: DiffMono: "521.884074" xref: Formula: "C 13 H 16 Mo 1 N 6 O 9 P 1 S 3" xref: MassAvg: "623.43" xref: MassMono: "624.893259" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00744 ! molybdenum pterin containing modification is_a: MOD:00861 ! phosphorus containing residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00152 name: S-(8alpha-FAD)-L-cysteine namespace: PSI-MOD def: "modification from RESID" [PubMed:10220347, RESID:AA0143, UniMod:50] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "8alpha-(S-cysteinyl)FAD" EXACT RESID-alternate [] synonym: "FAD" RELATED PSI-MS-label [] synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] synonym: "S-8alpha-FAD cysteine" EXACT UniProt-feature [] synonym: "S8aFADCys" EXACT PSI-MOD-short [] xref: DiffAvg: "783.53" xref: DiffFormula: "C 27 H 31 N 9 O 15 P 2 S 0" xref: DiffMono: "783.141485" xref: Formula: "C 30 H 36 N 10 O 16 P 2 S 1" xref: MassAvg: "886.68" xref: MassMono: "886.150669" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00895 ! FAD modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00153 name: 3'-(8alpha-FAD)-L-histidine namespace: PSI-MOD def: "modification from RESID" [PubMed:241294, PubMed:8076, RESID:AA0144, UniMod:50] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(3-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "8alpha-(N(delta)-histidyl)FAD" EXACT RESID-alternate [] synonym: "8alpha-(N3'-histidyl)FAD" EXACT RESID-alternate [] synonym: "8alpha-N1-histidyl FAD [misnomer]" RELATED RESID-misnomer [] synonym: "FAD" RELATED PSI-MS-label [] synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] synonym: "Npros8aFADHis" EXACT PSI-MOD-short [] synonym: "pi-(8alpha-FAD)-histidine" EXACT RESID-alternate [] synonym: "pros-(8alpha-FAD)-histidine" EXACT RESID-alternate [] synonym: "Pros-8alpha-FAD histidine" EXACT UniProt-feature [] xref: DiffAvg: "783.53" xref: DiffFormula: "C 27 H 31 N 9 O 15 P 2" xref: DiffMono: "783.141485" xref: Formula: "C 33 H 38 N 12 O 16 P 2" xref: MassAvg: "920.67" xref: MassMono: "920.200396" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00895 ! FAD modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00154 name: O4'-(8alpha-FAD)-L-tyrosine namespace: PSI-MOD def: "modification from RESID" [DeltaMass:0, PubMed:7391034, RESID:AA0145, UniMod:50] comment: From DeltaMass: Average Mass: 783 subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(4-[8alpha-riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]oxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "8alpha-(O4'-tyrosyl)FAD" EXACT RESID-alternate [] synonym: "FAD" RELATED PSI-MS-label [] synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] synonym: "O-8 alpha-Flavin [FAD])- (of Tyrosine)" EXACT DeltaMass-label [] synonym: "O-8alpha-FAD tyrosine" EXACT UniProt-feature [] synonym: "O8aFADTyr" EXACT PSI-MOD-short [] xref: DiffAvg: "783.53" xref: DiffFormula: "C 27 H 31 N 9 O 15 P 2" xref: DiffMono: "783.141485" xref: Formula: "C 36 H 40 N 10 O 17 P 2" xref: MassAvg: "946.71" xref: MassMono: "946.204813" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00895 ! FAD modified residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00155 name: 3'-hydroxylation of L-tyrosine to L-3',4'-dihydroxyphenylalanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to L-3',4'-dihydroxyphenylalanine." [DeltaMass:0, PubMed:1610822, PubMed:1903612, PubMed:3734192, RESID:AA0146] comment: incidental to RESID:AA0368 From DeltaMass: Average Mass: 16 subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(3,4-dihydroxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "3',4'-dihydroxyphenylalanine" EXACT UniProt-feature [] synonym: "3,4-Dihydroxy-Phenylalanine (from Tyrosine) (DOPA)" EXACT DeltaMass-label [] synonym: "3HyTyr" EXACT PSI-MOD-short [] synonym: "L-3'-hydroxytyrosine" EXACT RESID-alternate [] synonym: "L-DOPA" EXACT RESID-alternate [] synonym: "levodopa" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 9 H 9 N 1 O 3" xref: MassAvg: "179.17" xref: MassMono: "179.058243" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00707 ! hydroxylated tyrosine [Term] id: MOD:00156 name: oxidation of tyrosine to L-2',4',5'-topaquinone namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to an L-2',4',5'-topaquinone." [ChEBI:21187, PubMed:10387067, PubMed:1457410, PubMed:1569055, PubMed:2111581, RESID:AA0147, UniMod:392] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(5-hydroxy-2,5-cyclohexadien-1,4-dion-2-yl)propanoic acid" EXACT RESID-systematic [] synonym: "2',4',5'-topaquinone" EXACT UniProt-feature [] synonym: "2,4,5-trihydroxyphenylalanine quinone" EXACT RESID-alternate [] synonym: "5-(2-carboxy-2-aminoethyl)-2-hydroxy-1,4-benzoquinone" EXACT RESID-alternate [] synonym: "L-2,4,5-TOPAquinone" EXACT RESID-alternate [] synonym: "Quinone" RELATED PSI-MS-label [] synonym: "quinone" RELATED UniMod-description [] synonym: "TopaQ" EXACT PSI-MOD-short [] xref: DiffAvg: "29.98" xref: DiffFormula: "C 0 H -2 N 0 O 2" xref: DiffMono: "29.974179" xref: Formula: "C 9 H 7 N 1 O 4" xref: MassAvg: "193.16" xref: MassMono: "193.037508" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00157 name: oxidation of tryptophan to L-tryptophyl quinone namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to an L-tryptophan quinone." [DeltaMass:0, PubMed:2028257, RESID:AA0148, UniMod:392] comment: incidental to RESID:AA0149; incidental to RESID:AA0313; From DeltaMass: Average Mass: 30. subset: PSI-MOD_slim synonym: "(S)-3-(2-amino-2-carboxyethyl)-6,7-indolinedione" EXACT RESID-systematic [] synonym: "6,7 Dione (from Tryptophan)" EXACT DeltaMass-label [] synonym: "Quinone" RELATED PSI-MS-label [] synonym: "quinone" RELATED UniMod-description [] synonym: "TQ" EXACT PSI-MOD-short [] synonym: "Tryptophylquinone" EXACT UniProt-feature [] xref: DiffAvg: "29.98" xref: DiffFormula: "C 0 H -2 N 0 O 2" xref: DiffMono: "29.974179" xref: Formula: "C 11 H 8 N 2 O 3" xref: MassAvg: "216.19" xref: MassMono: "216.053492" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00679 ! carbon oxygenated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00158 name: 4'-(L-tryptophan)-L-tryptophyl quinone namespace: PSI-MOD def: "A protein modification that effectively converts two L-tryptophan residues to 4'-(L-tryptophan)-L-tryptophyl quinone." [ChEBI:20251, DeltaMass:0, PubMed:2028257, RESID:AA0149] comment: Cross-link 2; secondary to RESID:AA0148; From DeltaMass: Average Mass: 28. subset: PSI-MOD_slim synonym: "(S,S)-3-(2-amino-2-carboxyethyl)-4-[3-(2-amino-2-carboxyethyl)-1H-indol-2-yl]-6,7-indolinedione" EXACT RESID-systematic [] synonym: "2,4-BisTrp-6,7-dione (from Tryptophan)" EXACT DeltaMass-label [] synonym: "4'-tryptophan-tryptophylquinone" EXACT RESID-alternate [] synonym: "4-(2'-tryptophyl)tryptophan-6,7-dione" EXACT RESID-alternate [] synonym: "alpha,alpha'-diamino-6',7'-dihydro-6',7'-dioxo-(2,4'-bi-1H-indole)-3,3'-dipropanoic acid" EXACT RESID-alternate [] synonym: "Tryptophan tryptophylquinone (Trp-Trp)" EXACT UniProt-feature [] xref: DiffAvg: "27.97" xref: DiffFormula: "C 0 H -4 N 0 O 2" xref: DiffMono: "27.958529" xref: Formula: "C 22 H 16 N 4 O 4" xref: MassAvg: "400.39" xref: MassMono: "400.117155" xref: Origin: "W, W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00159 name: O-phosphopantetheine-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-phosphopantetheine-L-serine." [DeltaMass:0, PubMed:10320345, PubMed:10997907, PubMed:12057197, PubMed:12869567, PubMed:4568609, RESID:AA0150, UniMod:49] comment: UniMod has DiffFormula C 11 H 20 N 2 O 6 P 1 S 1 From DeltaMass: Average Mass: 339 subset: PSI-MOD_slim synonym: "(2R)-4-((2S)-2-amino-2-carboxyethyl)phosphonato-2-hydroxy-N-[3-(2-sulfanylethyl)amino-3-oxopropyl]-3,3-dimethylbutanamide" EXACT RESID-systematic [] synonym: "4'-Phosphopantetheine" EXACT DeltaMass-label [] synonym: "Phosphopantetheine" RELATED PSI-MS-label [] synonym: "Phosphopantetheine" RELATED UniMod-description [] synonym: "Phosphopantetheine (covalent)" EXACT UniProt-feature [] xref: DiffAvg: "340.33" xref: DiffFormula: "C 11 H 21 N 2 O 6 P 1 S 1" xref: DiffMono: "340.085794" xref: Formula: "C 14 H 26 N 3 O 8 P 1 S 1" xref: MassAvg: "427.41" xref: MassMono: "427.117822" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00861 ! phosphorus containing residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00160 name: N4-glycosyl-L-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to an N4-glycosyl-L-asparagine." [PubMed:111247, PubMed:1694179, PubMed:5490222, RESID:AA0151] subset: PSI-MOD_slim synonym: "N-linked (GlcNAc)" EXACT UniProt-feature [] synonym: "N4GlycoAsn" EXACT PSI-MOD-short [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" xref: Formula: "C 12 H 19 N 3 O 7" xref: MassAvg: "317.30" xref: MassMono: "317.122300" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00006 ! N-glycosylated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00161 name: S-glucosyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-glucosylated L-cysteine." [PubMed:1145128, PubMed:15279557, PubMed:5286858, RESID:AA0152, UniMod:41] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(beta-D-glucopyranosylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "Hex" RELATED PSI-MS-label [] synonym: "Hexose" RELATED UniMod-description [] synonym: "S-(beta-D-glucopyranosyl)cysteine" EXACT RESID-alternate [] synonym: "S-glycosyl-cysteine" EXACT RESID-alternate [] synonym: "S-linked (Glc)" EXACT UniProt-feature [] synonym: "SGlcCys" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5 S 0" xref: DiffMono: "162.052823" xref: Formula: "C 9 H 15 N 1 O 6 S 1" xref: MassAvg: "265.28" xref: MassMono: "265.062008" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00426 ! S-glycosylated residue is_a: MOD:00433 ! glucosylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00162 name: O5-glucosylgalactosyl-L-hydroxylysine namespace: PSI-MOD def: "modification from RESID" [PubMed:15149698, PubMed:4288358, PubMed:4319110, RESID:AA0153, UniMod:393] comment: secondary to RESID:AA0028 subset: PSI-MOD_slim synonym: "(2S,5R)-2,6-diamino-5-[4,5-dihydroxy-6-(hydroxymethyl)-3-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-oxan-2-yl]oxy-hexanoic acid" EXACT RESID-systematic [] synonym: "5-[(2-O-alpha-D-glucopyranosyl-beta-D-galactopyranosyl)oxy]-L-lysine" EXACT RESID-alternate [] synonym: "Glucosylgalactosyl" RELATED PSI-MS-label [] synonym: "glucosylgalactosyl hydroxylysine" RELATED UniMod-description [] synonym: "O-linked (Gal-Glc)" EXACT UniProt-feature [] synonym: "OGlcGal5HyLys" EXACT PSI-MOD-short [] xref: DiffAvg: "340.28" xref: DiffFormula: "C 12 H 20 N 0 O 11" xref: DiffMono: "340.100561" xref: Formula: "C 18 H 32 N 2 O 12" xref: MassAvg: "468.45" xref: MassMono: "468.195524" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00396 ! O-glycosylated residue is_a: MOD:00476 ! galactosylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00163 name: O-(N-acetylaminogalactosyl)-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:115869, PubMed:16005634, PubMed:3086323, PubMed:8948436, PubMed:9092502, RESID:AA0154, UniMod:43] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(alpha-D-2-acetamido-2-deoxygalactopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "mucin type O-glycosylserine" EXACT RESID-alternate [] synonym: "N-Acetylhexosamine" RELATED UniMod-description [] synonym: "O-linked (GalNAc)" EXACT UniProt-feature [] synonym: "O3-(N-acetylgalactosaminyl)serine" EXACT RESID-alternate [] synonym: "OGalNAcSer" EXACT PSI-MOD-short [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" xref: Formula: "C 11 H 18 N 2 O 7" xref: MassAvg: "290.27" xref: MassMono: "290.111401" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine is_a: MOD:00563 ! N-acetylaminogalactosylated residue [Term] id: MOD:00164 name: O-(N-acetylaminogalactosyl)-L-threonine namespace: PSI-MOD def: "modification from RESID" [PubMed:16005634, PubMed:1997327, PubMed:3086323, PubMed:8948436, PubMed:9092502, RESID:AA0155, UniMod:43] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-(alpha-D-2-acetamido-2-deoxygalactopyranosyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "HexNAc" RELATED PSI-MS-label [] synonym: "mucin type O-glycosylthreonine" EXACT RESID-alternate [] synonym: "N-Acetylhexosamine" RELATED UniMod-description [] synonym: "O-linked (GalNAc)" EXACT UniProt-feature [] synonym: "O3-(N-acetylgalactosaminyl)threonine" EXACT RESID-alternate [] synonym: "OGalNAcThr" EXACT PSI-MOD-short [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" xref: Formula: "C 12 H 20 N 2 O 7" xref: MassAvg: "304.30" xref: MassMono: "304.127051" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00005 ! O-glycosyl-L-threonine is_a: MOD:00563 ! N-acetylaminogalactosylated residue [Term] id: MOD:00165 name: 1'-mannosyl-L-tryptophan namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to 1'-mannosyl-L-tryptophan." [PubMed:1482345, PubMed:16150691, RESID:AA0156] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1-D-mannopyranosyloxy-1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "1'-glycosyl-L-tryptophan" EXACT RESID-alternate [] synonym: "N-linked (Man)" EXACT UniProt-feature [] synonym: "N-mannosyl-tryptophan" EXACT RESID-alternate [] synonym: "N1'ManTrp" EXACT PSI-MOD-short [] synonym: "N1-mannosyl-tryptophan" EXACT RESID-alternate [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 17 H 20 N 2 O 6" xref: MassAvg: "348.35" xref: MassMono: "348.132136" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00006 ! N-glycosylated residue is_a: MOD:00595 ! mannosylated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00166 name: O4'-glucosyl-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to O4'-glucosyl-tyrosine." [PubMed:15279557, PubMed:3181138, RESID:AA0157, UniMod:41] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(4-alpha-glucopyranosyloxy)phenylpropanoic acid" EXACT RESID-systematic [] synonym: "Hex" RELATED PSI-MS-label [] synonym: "Hexose" RELATED UniMod-description [] synonym: "O4'-glycosyl-L-tyrosine" EXACT RESID-alternate [] synonym: "O4GlcTyr" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 15 H 19 N 1 O 7" xref: MassAvg: "325.31" xref: MassMono: "325.116152" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00396 ! O-glycosylated residue is_a: MOD:00433 ! glucosylated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00167 name: N-asparaginyl-glycosylphosphatidylinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to N-asparaginyl-glycosylphosphatidylinositolethanolamine." [PubMed:1824714, PubMed:8276756, RESID:AA0158] subset: PSI-MOD_slim synonym: "GPI-anchor amidated asparagine" EXACT UniProt-feature [] synonym: "GPIAsn" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 6 H 13 N 3 O 6 P 1" xref: MassAvg: "254.16" xref: MassMono: "254.054197" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00168 name: N-aspartyl-glycosylphosphatidylinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to N-(aspart-1-yl)-glycosylphosphatidylinositolethanolamine." [PubMed:7120400, RESID:AA0159] subset: PSI-MOD_slim synonym: "GPI-anchor amidated aspartate" EXACT UniProt-feature [] synonym: "GPIAsp" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 6 H 12 N 2 O 7 P 1" xref: MassAvg: "255.14" xref: MassMono: "255.038212" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00169 name: N-cysteinyl-glycosylphosphatidylinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to N-cysteinyl-glycosylphosphatidylinositolethanolamine." [PubMed:2897081, RESID:AA0160] subset: PSI-MOD_slim synonym: "GPI-anchor amidated cysteine" EXACT UniProt-feature [] synonym: "GPICys" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1 S 0" xref: DiffMono: "123.008530" xref: Formula: "C 5 H 12 N 2 O 5 P 1 S 1" xref: MassAvg: "243.20" xref: MassMono: "243.020454" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00170 name: N-glycyl-glycosylphosphatidylinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-glycyl-glycosylphosphatidylinositolethanolamine." [PubMed:2341397, RESID:AA0161] subset: PSI-MOD_slim synonym: "GPI-anchor amidated glycine" EXACT UniProt-feature [] synonym: "GPIGly" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 4 H 10 N 2 O 5 P 1" xref: MassAvg: "197.11" xref: MassMono: "197.032733" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00171 name: N-seryl-glycosylphosphatidylinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to N-seryl-glycosylphosphatidylinositolethanolamine." [PubMed:2111324, PubMed:8448158, RESID:AA0162] subset: PSI-MOD_slim synonym: "GPI-anchor amidated serine" EXACT UniProt-feature [] synonym: "GPISer" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 5 H 12 N 2 O 6 P 1" xref: MassAvg: "227.13" xref: MassMono: "227.043298" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00172 name: N-alanyl-glycosylphosphatidylinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to N-alanyl-glycosylphosphatidylinositolethanolamine." [PubMed:7682556, PubMed:7744038, RESID:AA0163] subset: PSI-MOD_slim synonym: "GPI-anchor amidated alanine" EXACT UniProt-feature [] synonym: "GPIAla" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 5 H 12 N 2 O 5 P 1" xref: MassAvg: "211.13" xref: MassMono: "211.048383" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00901 ! modified L-alanine residue [Term] id: MOD:00173 name: N-threonyl-glycosylphosphatidylinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to N-threonyl-glycosylphosphatidylinositolethanolamine." [RESID:AA0164] subset: PSI-MOD_slim synonym: "GPI-anchor amidated threonine" EXACT UniProt-feature [] synonym: "GPIThr" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 6 H 14 N 2 O 6 P 1" xref: MassAvg: "241.16" xref: MassMono: "241.058948" xref: Origin: "T" xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00818 ! glycosylphosphatidylinositolated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00174 name: N-glycyl-glycosylsphingolipidinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-glycyl-glycosylsphingolipidinositolethanolamine." [PubMed:12626404, PubMed:8404891, RESID:AA0165] subset: PSI-MOD_slim synonym: "GPI-like-anchor amidated glycine" EXACT UniProt-feature [] synonym: "GSIGly" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 4 H 10 N 2 O 5 P 1" xref: MassAvg: "197.11" xref: MassMono: "197.032733" xref: Origin: "G" xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00175 name: N-seryl-glycosylsphingolipidinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to N-seryl-glycosylsphingolipidinositolethanolamine." [PubMed:12626404, PubMed:2721485, PubMed:8269952, RESID:AA0166] subset: PSI-MOD_slim synonym: "GPI-like-anchor amidated serine" EXACT UniProt-feature [] synonym: "GSISer" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 5 H 12 N 2 O 6 P 1" xref: MassAvg: "227.13" xref: MassMono: "227.043298" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00176 name: O-(phosphoribosyl dephospho-coenzyme A)-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:10924139, PubMed:11052675, PubMed:179809, PubMed:180526, PubMed:368065, RESID:AA0167, UniMod:395] comment: pRibodePcoA subset: PSI-MOD_slim synonym: "O3-(phosphate-5-ribosyl-alpha-2-adenosine-5-diphosphate pantetheine)-L-serine" EXACT RESID-alternate [] synonym: "O3-(phosphoribosyl dephospho-coenzyme A)-L-serine" EXACT RESID-alternate [] synonym: "O3-2'-(5''-phosphoribosyl-3'-dephosphocoenzyme A)-L-serine" EXACT RESID-alternate [] synonym: "phosphoribosyl dephospho-coenzyme A" RELATED UniMod-description [] synonym: "Phosphoribosyl dephospho-coenzyme A (covalent)" EXACT UniProt-feature [] synonym: "PhosphoribosyldephosphoCoA" RELATED PSI-MS-label [] xref: DiffAvg: "881.63" xref: DiffFormula: "C 26 H 42 N 7 O 19 P 3 S 1" xref: DiffMono: "881.146903" xref: Formula: "C 29 H 47 N 8 O 21 P 3 S 1" xref: MassAvg: "968.71" xref: MassMono: "968.178931" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00177 name: omega-N-(ADP-ribosyl)-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-argininine residue to omega-N-(ADP-ribosyl)-L-arginine." [DeltaMass:0, PubMed:15842200, PubMed:209022, PubMed:3090031, PubMed:3923473, PubMed:6582062, RESID:AA0168, UniMod:213] comment: From DeltaMass: Average Mass: 541. subset: PSI-MOD_slim synonym: "(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid" EXACT RESID-systematic [] synonym: "ADP Ribose addition" RELATED UniMod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "ADP-ribosylarginine" EXACT UniProt-feature [] synonym: "N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine" EXACT RESID-alternate [] synonym: "N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT RESID-alternate [] synonym: "N-(ADP-ribosyl)- (on Arginine)" EXACT DeltaMass-label [] xref: DiffAvg: "541.30" xref: DiffFormula: "C 15 H 21 N 5 O 13 P 2" xref: DiffMono: "541.061109" xref: Formula: "C 21 H 33 N 9 O 14 P 2" xref: MassAvg: "697.49" xref: MassMono: "697.162220" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00178 name: S-(ADP-ribosyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-(ADP-ribosyl)-L-cysteine." [DeltaMass:0, PubMed:15842200, PubMed:3863818, RESID:AA0169, UniMod:213] comment: From DeltaMass: Average Mass: 541. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "ADP Ribose addition" RELATED UniMod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "ADP-ribosylcysteine" EXACT UniProt-feature [] synonym: "S-(ADP-ribosyl)- (on Cysteine)" EXACT DeltaMass-label [] synonym: "S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT RESID-alternate [] synonym: "S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT RESID-alternate [] xref: DiffAvg: "541.30" xref: DiffFormula: "C 15 H 21 N 5 O 13 P 2 S 0" xref: DiffMono: "541.061109" xref: Formula: "C 18 H 26 N 6 O 14 P 2 S 1" xref: MassAvg: "644.44" xref: MassMono: "644.070294" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00179 name: L-glutamyl 5-glycerylphosphorylethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamyl 5-glycerylphosphorylethanolamine." [PubMed:2511205, PubMed:2569467, PubMed:9662537, RESID:AA0170, UniMod:396] comment: glycerylPE subset: PSI-MOD_slim synonym: "(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid" EXACT RESID-systematic [] synonym: "GlycerylPE" RELATED PSI-MS-label [] synonym: "glycerylphosphorylethanolamine" RELATED UniMod-description [] synonym: "Glycerylphosphorylethanolamine (covalent)" EXACT UniProt-feature [] synonym: "L-glutamyl 5-glycerophosphoethanolamine" EXACT RESID-alternate [] synonym: "L-glutamyl 5-glycerophosphorylethanolamine" EXACT RESID-alternate [] xref: DiffAvg: "197.13" xref: DiffFormula: "C 5 H 12 N 1 O 5 P 1" xref: DiffMono: "197.045309" xref: Formula: "C 10 H 19 N 2 O 8 P 1" xref: MassAvg: "326.24" xref: MassMono: "326.087902" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00180 name: S-sulfo-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-sulfo-L-cysteine." [PubMed:12876326, PubMed:14752058, PubMed:643076, RESID:AA0171, UniMod:40] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(sulfosulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(sulfothio)propanoic acid" EXACT RESID-alternate [] synonym: "cysteine sulfate thioester" EXACT RESID-alternate [] synonym: "O-Sulfonation" RELATED UniMod-description [] synonym: "S-sulfocysteine" EXACT PSI-MOD-alternate [] synonym: "S-sulfocysteine" EXACT RESID-alternate [] synonym: "Sulfo" RELATED PSI-MS-label [] xref: DiffAvg: "80.06" xref: DiffFormula: "C 0 H 0 N 0 O 3 S 1" xref: DiffMono: "79.956815" xref: Formula: "C 3 H 5 N 1 O 4 S 2" xref: MassAvg: "183.21" xref: MassMono: "182.966000" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00695 ! sulfated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00181 name: O4'-sulfo-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to O4'-sulfo-L-tyrosine." [DeltaMass:88, PubMed:10226369, PubMed:14752058, PubMed:2303439, PubMed:3778455, PubMed:3801003, RESID:AA0172, UniMod:40] comment: From DeltaMass: Average Mass: 80 Average Mass Change:80 PubMed:9624161. subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate" EXACT RESID-alternate [] synonym: "O-Sulfonation" RELATED UniMod-description [] synonym: "O4-sulfotyrosine" EXACT RESID-alternate [] synonym: "Sulfo" RELATED PSI-MS-label [] synonym: "Sulfotyrosine" EXACT UniProt-feature [] synonym: "Sulphation (of O of Tyrosine)" EXACT DeltaMass-label [] synonym: "tyrosine sulfate" EXACT RESID-alternate [] synonym: "tyrosine-O-sulfonic acid" EXACT RESID-alternate [] synonym: "tyrosine-O-sulphonic acid" EXACT RESID-alternate [] synonym: "Tyrosinyl Sulphate [misnomer]" EXACT DeltaMass-label [] xref: DiffAvg: "80.06" xref: DiffFormula: "C 0 H 0 N 0 O 3 S 1" xref: DiffMono: "79.956815" xref: Formula: "C 9 H 9 N 1 O 5 S 1" xref: MassAvg: "243.24" xref: MassMono: "243.020143" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00695 ! sulfated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00182 name: L-bromohistidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to L-bromohistidine." [PubMed:2076468, PubMed:9033387, RESID:AA0173, UniMod:340] subset: PSI-MOD_slim synonym: "Br1His" EXACT PSI-MOD-short [] synonym: "bromination" RELATED UniMod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "Bromohistidine" EXACT UniProt-feature [] xref: DiffAvg: "78.90" xref: DiffFormula: "Br 1 C 0 H -1 N 0 O 0" xref: DiffMono: "77.910512" xref: Formula: "Br 1 C 6 H 6 N 3 O 1" xref: MassAvg: "216.04" xref: MassMono: "214.969424" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00754 ! brominated residue [Term] id: MOD:00183 name: L-2'-bromophenylalanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-phenylalanine residue to L-2'-bromophenylalanine." [DeltaMass:83, PubMed:2059627, PubMed:2076468, PubMed:9033387, RESID:AA0174, UniMod:340] comment: From DeltaMass: Average Mass: 78 Average Mass Change:78 References:Yoshino,K et.al. Biochemistry Vol. 30 pg 6203-9 (1991) Identifidation of a novel amino acid, o-bromo-L-phenylananine, in egg-associated peptides that activate spermatozoa. subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(2-bromophenyl)propanoic acid" EXACT RESID-systematic [] synonym: "2'-BrPhe" EXACT PSI-MOD-short [] synonym: "bromination" RELATED UniMod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "L-o-bromination of Phe with 79Br" EXACT DeltaMass-label [] synonym: "o-bromophenylalanine" EXACT RESID-alternate [] synonym: "ortho-bromophenylalanine" EXACT RESID-alternate [] xref: DiffAvg: "78.90" xref: DiffFormula: "Br 1 C 0 H -1 N 0 O 0" xref: DiffMono: "77.910512" xref: Formula: "Br 1 C 9 H 8 N 1 O 1" xref: MassAvg: "226.07" xref: MassMono: "224.978926" xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00972 ! monobrominated L-phenylalanine [Term] id: MOD:00184 name: L-3'-bromophenylalanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-phenylalanine residue to L-3'-bromophenylalanine." [PubMed:2076468, PubMed:9033387, RESID:AA0175, UniMod:340] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(3-bromophenyl)propanoic acid" EXACT RESID-systematic [] synonym: "3'-BrPhe" EXACT PSI-MOD-short [] synonym: "bromination" RELATED UniMod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "m-bromophenylalanine" EXACT RESID-alternate [] synonym: "meta-bromophenylalanine" EXACT RESID-alternate [] xref: DiffAvg: "78.90" xref: DiffFormula: "Br 1 C 0 H -1 N 0 O 0" xref: DiffMono: "77.910512" xref: Formula: "Br 1 C 9 H 8 N 1 O 1" xref: MassAvg: "226.07" xref: MassMono: "224.978926" xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00972 ! monobrominated L-phenylalanine [Term] id: MOD:00185 name: L-4'-bromophenylalanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-phenylalanine residue to L-4'-bromophenylalanine." [PubMed:2076468, PubMed:9033387, RESID:AA0176, UniMod:340] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(4-bromophenyl)propanoic acid" EXACT RESID-systematic [] synonym: "4'-BrPhe" EXACT PSI-MOD-short [] synonym: "bromination" RELATED UniMod-description [] synonym: "Bromo" RELATED PSI-MS-label [] synonym: "p-bromophenylalanine" EXACT RESID-alternate [] synonym: "para-bromophenylalanine" EXACT RESID-alternate [] xref: DiffAvg: "78.90" xref: DiffFormula: "Br 1 C 0 H -1 N 0 O 0" xref: DiffMono: "77.910512" xref: Formula: "Br 1 C 9 H 8 N 1 O 1" xref: MassAvg: "226.07" xref: MassMono: "224.978926" xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00972 ! monobrominated L-phenylalanine [Term] id: MOD:00186 name: 3',3'',5'-triiodo-L-thyronine namespace: PSI-MOD def: "A protein modification that effectively substitutes an L-tyrosine residue with 3',3'',5'-triiodo-L-thyronine." [ChEBI:18258, DeltaMass:0, RESID:AA0177, UniMod:397] comment: From DeltaMass: Average Mass: 470 subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[4-(4-hydroxy-3-iodophenoxy)-3,5-diiodophenyl]propanoic acid" EXACT RESID-systematic [] synonym: "3,3',5-triiodo-L-thyronine" EXACT RESID-alternate [] synonym: "3,5,3'-triiodo-L-thyronine" EXACT RESID-alternate [] synonym: "3,5,3'-Triiodothyronine (from Tyrosine)" EXACT DeltaMass-label [] synonym: "4-(4-hydroxy-3-iodophenoxy)-3,5-diiodo-L-phenylalanine" EXACT RESID-alternate [] synonym: "liothyronine" EXACT RESID-alternate [] synonym: "O-(4-hydroxy-3-iodophenyl)-3,5-diiodo-L-tyrosine" EXACT RESID-alternate [] synonym: "triiodo" RELATED UniMod-description [] synonym: "Triiodothyronine" EXACT UniProt-feature [] synonym: "Triiodothyronine" RELATED PSI-MS-label [] xref: DiffAvg: "469.78" xref: DiffFormula: "C 6 H 1 I 3 N 0 O 1" xref: DiffMono: "469.716158" xref: Formula: "C 15 H 10 I 3 N 1 O 3" xref: MassAvg: "632.96" xref: MassMono: "632.779486" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00502 ! triiodinated residue is_a: MOD:00998 ! iodinated tyrosine [Term] id: MOD:00187 name: L-thyroxine namespace: PSI-MOD def: "A protein modification that effectively substitutes an L-tyrosine residue with L-thyroxine." [ChEBI:18332, PubMed:6704086, RESID:AA0178, UniMod:398] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodophenyl]propanoic acid" EXACT RESID-systematic [] synonym: "3',3'',5',5''-tetraiodo-L-thyronine" EXACT RESID-alternate [] synonym: "3,3',5,5'-tetraiodo-L-thyronine" EXACT RESID-alternate [] synonym: "3,5,3',5'-tetraiodo-L-thyronine" EXACT RESID-alternate [] synonym: "4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodo-L-phenylalanine" EXACT RESID-alternate [] synonym: "O-(4-hydroxy-3,5-diiodophenyl)-3,5-diiodo-L-tyrosine" EXACT RESID-alternate [] synonym: "tetraiodo" RELATED UniMod-description [] synonym: "Thyroxine" EXACT UniProt-feature [] synonym: "Thyroxine" RELATED PSI-MS-label [] xref: DiffAvg: "595.68" xref: DiffFormula: "C 6 H 0 I 4 N 0 O 1" xref: DiffMono: "595.612805" xref: Formula: "C 15 H 9 I 4 N 1 O 3" xref: MassAvg: "758.85" xref: MassMono: "758.676134" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00998 ! iodinated tyrosine [Term] id: MOD:00188 name: L-6'-bromotryptophan namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to L-6'-bromotryptophan." [PubMed:12118011, PubMed:9030520, PubMed:9033387, PubMed:9434739, RESID:AA0179, UniMod:340] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(6-bromo-1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "6'-bromotryptophan" EXACT UniProt-feature [] synonym: "6'-BrTrp" EXACT PSI-MOD-short [] synonym: "bromination" RELATED UniMod-description [] synonym: "Bromo" RELATED PSI-MS-label [] xref: DiffAvg: "78.90" xref: DiffFormula: "Br 1 C 0 H -1 N 0 O 0" xref: DiffMono: "77.910512" xref: Formula: "Br 1 C 11 H 9 N 2 O 1" xref: MassAvg: "265.11" xref: MassMono: "263.989825" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00754 ! brominated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00189 name: dehydroalanine (Ser) namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to dehydroalanine." [DeltaMass:0, PubMed:10220322, PubMed:1547888, PubMed:1815586, PubMed:2914619, PubMed:7947813, PubMed:8239649, RESID:AA0181, UniMod:23] subset: PSI-MOD_slim synonym: "2,3-didehydroalanine (Ser)" EXACT UniProt-feature [] synonym: "dHAla(Ser)" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 3 H 3 N 1 O 1" xref: MassAvg: "69.06" xref: MassMono: "69.021464" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00416 ! phosphorylation of an hydroxyl amino acid with prompt loss of phosphate is_a: MOD:00704 ! dehydrated residue is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01168 ! dehydroalanine [Term] id: MOD:00190 name: dehydrobutyrine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to dehydrobutyrine" [DeltaMass:0, PubMed:1547888, PubMed:3769923, RESID:AA0182, UniMod:23] subset: PSI-MOD_slim synonym: "2,3-didehydrobutyrine" EXACT UniProt-feature [] synonym: "2,3-didehydrobutyrine" EXACT RESID-alternate [] synonym: "2-amino-butenoic acid" EXACT RESID-systematic [] synonym: "alpha,beta-dehydroaminobutyric acid" EXACT RESID-alternate [] synonym: "anhydrothreonine" EXACT RESID-alternate [] synonym: "Dehydrated" RELATED UniMod-interim [] synonym: "Dehydration" RELATED UniMod-description [] synonym: "Dehydroamino butyric acid" EXACT DeltaMass-label [] synonym: "dHyThr" EXACT PSI-MOD-short [] synonym: "methyl-dehydroalanine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 4 H 5 N 1 O 1" xref: MassAvg: "83.09" xref: MassMono: "83.037114" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00416 ! phosphorylation of an hydroxyl amino acid with prompt loss of phosphate is_a: MOD:00704 ! dehydrated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00191 name: (Z)-2,3-didehydrotyrosine namespace: PSI-MOD def: "A protein modification that effectively converts L-tyrosine to (Z)-2,3-didehydrotyrosine." [PubMed:1347277, PubMed:9631087, RESID:AA0183, UniMod:401] comment: incidental to RESID:AA0184; incidental to RESID:AA0187; incidental to RESID:AA0188; incidental to RESID:AA0189; incidental to RESID:AA0378; incidental to RESID:AA0379; incidental to RESID:AA0380; incidental to RESID:AA0381 subset: PSI-MOD_slim synonym: "(Z)-2,3-didehydrogenated tyrosine" EXACT PSI-MOD-alternate [] synonym: "(Z)-2,3-didehydrotyrosine" EXACT UniProt-feature [] synonym: "(Z)-2-amino-3-(4-hydoxyphenyl)propenoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-oxo-butanoic_acid" RELATED UniMod-description [] synonym: "amino-(para-hydroxybenzylidenyl)acetic acid" EXACT RESID-alternate [] synonym: "cis-dehydrotyrosine" EXACT RESID-alternate [] synonym: "Didehydro" RELATED PSI-MS-label [] synonym: "green fluorescent protein chromophore" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] synonym: "red fluorescent protein chromophore" EXACT RESID-alternate [] synonym: "Z-dHTyr" EXACT PSI-MOD-short [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" xref: Formula: "C 9 H 7 N 1 O 2" xref: MassAvg: "161.16" xref: MassMono: "161.047678" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00706 ! dehydrogenated tyrosine [Term] id: MOD:00192 name: L-serine 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-serine residue and a glycine residue to form L-serine 5-imidazolinone glycine." [ChEBI:21393, PubMed:1347277, PubMed:9631087, RESID:AA0184] comment: Cross-link 2; carboxamidine; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "2-[(R)-1-amino-2-hydroxyethyl]-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "5-imidazolinone (Ser-Gly)" EXACT UniProt-feature [] synonym: "green fluorescent protein chromophore" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] synonym: "seryl-5-imidazolinone glycine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 5 H 6 N 2 O 2" xref: MassAvg: "126.11" xref: MassMono: "126.042927" xref: Origin: "G, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00908 ! modified glycine residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00193 name: L-3-oxoalanine (Cys) namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to L-oxoalanine." [DeltaMass:350, PubMed:14563551, PubMed:7628016, PubMed:8681943, PubMed:9478923, RESID:AA0185, UniMod:402] subset: PSI-MOD_slim synonym: "3-oxoalanine (Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-18.08" xref: DiffFormula: "C 0 H -2 N 0 O 1 S -1" xref: DiffMono: "-17.992806" xref: Formula: "C 3 H 3 N 1 O 2" xref: MassAvg: "85.06" xref: MassMono: "85.016378" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01169 ! L-3-oxoalanine [Term] id: MOD:00194 name: lactic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to an amino-terminal lactic acid." [PubMed:7607233, RESID:AA0186, UniMod:403] subset: PSI-MOD_slim synonym: "2-hydroxypropanoic acid" EXACT RESID-systematic [] synonym: "alpha-hydroxypropionic acid" EXACT RESID-alternate [] synonym: "Lactic acid" EXACT UniProt-feature [] synonym: "lactic acid from N-term Ser" RELATED UniMod-description [] synonym: "Ser->LacticAcid" RELATED PSI-MS-label [] xref: DiffAvg: "-15.01" xref: DiffFormula: "C 0 H -1 N -1 O 0" xref: DiffMono: "-15.010899" xref: Formula: "C 3 H 5 O 2" xref: MassAvg: "73.07" xref: MassMono: "73.028954" xref: Origin: "S" xref: TermSpec: "N-term" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00195 name: L-alanine 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-alanine residue and a glycine residue to form L-alanine 5-imidazolinone glycine." [PubMed:10220322, RESID:AA0187] comment: Cross-link 2; carboxamidine; incidental to RESID:AA0181; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "2-[(S)-1-aminoethyl]-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "4-methylidene-imidazole-5-one active site" EXACT RESID-alternate [] synonym: "5-imidazolinone (Ala-Gly)" EXACT UniProt-feature [] synonym: "alanyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 5 H 6 N 2 O 1" xref: MassAvg: "110.11" xref: MassMono: "110.048013" xref: Origin: "A, G" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00901 ! modified L-alanine residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00196 name: L-cysteine 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and a glycine residue to form L-cysteine 5-imidazolinone glycine." [PubMed:1537807, RESID:AA0188] comment: Cross-link 2; carboxamidine; incidental to RESID:AA0181; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "2-[(R)-1-amino-2-sulfanylethyl]-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "5-imidazolinone (Cys-Gly)" EXACT UniProt-feature [] synonym: "cysteinyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 5 H 6 N 2 O 1 S 1" xref: MassAvg: "142.18" xref: MassMono: "142.020084" xref: Origin: "C, G" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00197 name: 2-imino-glutamine 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-glutamine residue and a glycine residue to form 2-imino-glutamine 5-imidazolinone glycine." [PubMed:11050230, PubMed:11209050, RESID:AA0189] comment: Cross-link 2; carboxamidine; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "2,N-didehydroglutaminyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "2-(3-carbamoyl-1-imino-propyl)-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "2-iminomethyl-5-imidazolinone (Gln-Gly)" EXACT UniProt-feature [] synonym: "[2-(3-carbamoyl-1-imino-propyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid" EXACT RESID-alternate [] synonym: "fluorescent protein FP583 chromophore" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] synonym: "red fluorescent protein chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1" xref: DiffMono: "-20.026215" xref: Formula: "C 7 H 7 N 3 O 2" xref: MassAvg: "165.15" xref: MassMono: "165.053826" xref: Origin: "G, Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00907 ! modified L-glutamine residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00198 name: D-alanine (Ala) namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to D-alanine." [PubMed:15023056, PubMed:7287302, PubMed:7961627, RESID:AA0191] subset: PSI-MOD_slim synonym: "D-Ala(Ala)" EXACT PSI-MOD-short [] synonym: "D-alanine (Ala)" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 3 H 5 N 1 O 1" xref: MassAvg: "71.08" xref: MassMono: "71.037114" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00862 ! D-alanine is_a: MOD:00901 ! modified L-alanine residue [Term] id: MOD:00199 name: D-allo-isoleucine namespace: PSI-MOD def: "A protein modification that effectively converts an L-isoleucine residue to a D-allo-isoleucine." [ChEBI:30007, PubMed:8223491, RESID:AA0192] subset: PSI-MOD_slim synonym: "(2R,3S)-2-amino-3-methylpentanoic acid" EXACT RESID-systematic [] synonym: "D-allo-isoleucine" EXACT UniProt-feature [] synonym: "D-Ile" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 6 H 11 N 1 O 1" xref: MassAvg: "113.16" xref: MassMono: "113.084064" xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00910 ! modified L-isoleucine residue [Term] id: MOD:00200 name: D-methionine namespace: PSI-MOD def: "A protein modification that effectively converts an L-methionine residue to D-methionine." [ChEBI:29984, PubMed:16033333, PubMed:2542051, RESID:AA0193] subset: PSI-MOD_slim synonym: "(R)-2-amino-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-amino-4-(methylthio)butanoic acid" EXACT RESID-alternate [] synonym: "D-Met" EXACT PSI-MOD-short [] synonym: "D-methionine" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0 S 0" xref: DiffMono: "0.000000" xref: Formula: "C 5 H 9 N 1 O 1 S 1" xref: MassAvg: "131.20" xref: MassMono: "131.040485" xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00201 name: D-phenylalanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-phenylalanine residue to D-phenylalanine." [ChEBI:29996, PubMed:1548227, PubMed:1644179, PubMed:2597281, RESID:AA0194] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-phenylpropanoic acid" EXACT RESID-systematic [] synonym: "D-Phe" EXACT PSI-MOD-short [] synonym: "D-phenylalanine" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 9 H 9 N 1 O 1" xref: MassAvg: "147.17" xref: MassMono: "147.068414" xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:00202 name: D-serine (Ser) namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to D-serine." [PubMed:7973665, RESID:AA0195] subset: PSI-MOD_slim synonym: "D-Ser(Ser)" EXACT PSI-MOD-short [] synonym: "D-serine (Ser)" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 3 H 5 N 1 O 2" xref: MassAvg: "87.08" xref: MassMono: "87.032028" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00891 ! D-serine is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00203 name: D-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to D-asparagine." [ChEBI:29957, PubMed:1859408, RESID:AA0196] subset: PSI-MOD_slim synonym: "(R)-2-amino-4-butanediamic acid" EXACT RESID-systematic [] synonym: "D-alpha-aminosuccinamic acid" EXACT RESID-alternate [] synonym: "D-Asn" EXACT PSI-MOD-short [] synonym: "D-asparagine" EXACT UniProt-feature [] synonym: "D-aspartic acid beta-amide" EXACT RESID-alternate [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 4 H 6 N 2 O 2" xref: MassAvg: "114.10" xref: MassMono: "114.042927" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00204 name: D-leucine namespace: PSI-MOD def: "A protein modification that effectively converts an L-leucine residue to D-leucine." [ChEBI:30005, PubMed:10461743, PubMed:12135762, PubMed:1358533, PubMed:1548227, RESID:AA0197] subset: PSI-MOD_slim synonym: "(R)-2-amino-4-methylpentanoic acid" EXACT RESID-systematic [] synonym: "alpha-aminoisocaproic acid" EXACT RESID-alternate [] synonym: "D-Leu" EXACT PSI-MOD-short [] synonym: "D-leucine" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 6 H 11 N 1 O 1" xref: MassAvg: "113.16" xref: MassMono: "113.084064" xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00911 ! modified L-leucine residue [Term] id: MOD:00205 name: D-tryptophan namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to D-tryptophan." [ChEBI:29955, PubMed:8910408, RESID:AA0198] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-(3-indolyl)propionoic acid" EXACT RESID-alternate [] synonym: "D-Trp" EXACT PSI-MOD-short [] synonym: "D-tryptophan " EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 11 H 10 N 2 O 1" xref: MassAvg: "186.21" xref: MassMono: "186.079313" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00206 name: L-isoglutamyl-polyglycine namespace: PSI-MOD def: "modification from RESID" [ChEBI:21343, PubMed:10074368, PubMed:16368691, PubMed:7992051, RESID:AA0201] subset: PSI-MOD_slim synonym: "gamma-glutamylpolyglycine" EXACT RESID-alternate [] xref: DiffAvg: "57.05" xref: DiffFormula: "C 2 H 3 N 1 O 1" xref: DiffMono: "57.021464" xref: Formula: "C 7 H 10 N 2 O 4" xref: MassAvg: "186.17" xref: MassMono: "186.064057" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00207 name: L-isoglutamyl-polyglutamic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to isoglutamyl-polyglutamic acid, forming an isopeptide bond with a polyglutamic acid." [PubMed:10747868, PubMed:1680872, RESID:AA0202] subset: PSI-MOD_slim synonym: "gamma-glutamylpolyglutamic acid" EXACT RESID-alternate [] xref: DiffAvg: "129.11" xref: DiffFormula: "C 5 H 7 N 1 O 3" xref: DiffMono: "129.042593" xref: Formula: "C 10 H 14 N 2 O 6" xref: MassAvg: "258.23" xref: MassMono: "258.085186" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00208 name: O4'-(phospho-5'-adenosine)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-tyrosine residue and 5'-phosphoadenosine through a phosphodiester bond to form O4'-(phospho-5'-adenosine)-L-tyrosine." [DeltaMass:0, PubMed:5543675, RESID:AA0203, UniMod:405] comment: From DeltaMass: Average Mass: 329. subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[4-(5'-adenosine phosphonoxy)phenyl]propanoic acid" EXACT RESID-systematic [] synonym: "5'-adenylic-O-tyrosine" EXACT RESID-alternate [] synonym: "AMP binding site" RELATED UniMod-description [] synonym: "hydrogen 5'-adenylate tyrosine ester" EXACT RESID-alternate [] synonym: "O-5'-Adenosylation ( of Tyrosine)" EXACT DeltaMass-label [] synonym: "O-AMP-tyrosine" EXACT UniProt-feature [] synonym: "O4'-L-tyrosine 5'-adenosine phosphodiester" EXACT RESID-alternate [] synonym: "Phosphoadenosine" RELATED PSI-MS-label [] xref: DiffAvg: "329.21" xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1" xref: DiffMono: "329.052520" xref: Formula: "C 19 H 21 N 6 O 8 P 1" xref: MassAvg: "492.38" xref: MassMono: "492.115848" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01165 ! adenylated residue [Term] id: MOD:00209 name: S-(2-aminovinyl)-D-cysteine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-serine residue by a thioether bond to form S-(2-aminovinyl)-D-cysteine." [PubMed:3181159, PubMed:3769923, RESID:AA0204] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[((Z)-2-aminovinyl)sulfanyl]propanoic acid" EXACT RESID-systematic [] synonym: "(S,Z)-S-(2-aminovinyl)cysteine" EXACT RESID-alternate [] synonym: "S-(2-aminovinyl)-D-cysteine (Ser-Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-64.04" xref: DiffFormula: "C -1 H -4 N 0 O -3 S 0" xref: DiffMono: "-64.016044" xref: Formula: "C 5 H 7 N 2 O 1 S 1" xref: MassAvg: "143.19" xref: MassMono: "143.027909" xref: Origin: "C, S" xref: TermSpec: "C-term" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00210 name: oxidation to L-cysteine sulfenic acid namespace: PSI-MOD def: "A protein modification that effectively monooxygenates an L-cysteine residue to L-cysteine sulfenic acid." [DeltaMass:41, PubMed:10964927, PubMed:2501303, PubMed:8756456, PubMed:9214307, PubMed:9586994, PubMed:9587003, RESID:AA0205] comment: From DeltaMass: Average Mass: 16 Average Mass Change:16 Notes:Green et al. in J. B. C. 270, 18209-18211 (1995) quote Kim and Raines in Eur. J. Biochem. 224, 109-114 (1994). Kim and Raines using ESI-MS and sulfhydryl group titration found that bovine seminal ribonuclease contains a single oxidized sulfhydryl group, which cannot participate in a disulfide bond. This form of cysteine is called sulfenic acid (-SOH). subset: PSI-MOD_slim synonym: "(R)-2-amino-2-carboxyethanesulfenic acid" EXACT RESID-systematic [] synonym: "2-amino-3-sulfenopropanoic acid" EXACT RESID-alternate [] synonym: "3-sulfenoalanine" EXACT RESID-alternate [] synonym: "CysOH" EXACT PSI-MOD-short [] synonym: "Cysteine sulfenic acid (-SOH)" EXACT UniProt-feature [] synonym: "S-hydroxycysteine" EXACT RESID-alternate [] synonym: "Sulfenic Acid (from Cysteine)" EXACT DeltaMass-label [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1 S 0" xref: DiffMono: "15.994915" xref: Formula: "C 3 H 5 N 1 O 2 S 1" xref: MassAvg: "119.14" xref: MassMono: "119.004099" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00708 ! sulfur oxygenated L-cysteine [Term] id: MOD:00211 name: S-glycyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and a glycine residue by a thioester bond to form S-glycyl-L-cysteine." [ChEBI:22050, PubMed:3306404, RESID:AA0206] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(aminoacetyl)sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "glycine cysteine thioester" EXACT RESID-alternate [] synonym: "S-(2-amino-1-oxoethyl)cysteine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 5 H 7 N 2 O 2 S 1" xref: MassAvg: "159.19" xref: MassMono: "159.022823" xref: Origin: "C, G" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00908 ! modified glycine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00212 name: S-4-hydroxycinnamyl-L-cysteine namespace: PSI-MOD def: "modification from RESID" [PubMed:7947803, PubMed:7981196, RESID:AA0207, UniMod:407] subset: PSI-MOD_slim synonym: "(S,E)-2-amino-3-[3-(4-hydroxyphenyl)propenoylsulfanyl]propanoic acid" EXACT RESID-systematic [] synonym: "4-hydroxycinnamyl (covalent)" EXACT UniProt-feature [] synonym: "cinnamate cysteine thioester" EXACT RESID-alternate [] synonym: "Hydroxycinnamyl" RELATED PSI-MS-label [] synonym: "hydroxycinnamyl" RELATED UniMod-description [] synonym: "S-para-coumaryl-L-cysteine" EXACT RESID-alternate [] xref: DiffAvg: "146.14" xref: DiffFormula: "C 9 H 6 N 0 O 2 S 0" xref: DiffMono: "146.036779" xref: Formula: "C 12 H 11 N 1 O 3 S 1" xref: MassAvg: "249.29" xref: MassMono: "249.045964" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00213 name: chondroitin sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:1794445, PubMed:1898736, PubMed:3472204, RESID:AA0208] subset: PSI-MOD_slim synonym: "chondroitin 4-sulfate (chondroitin sulfate A)" EXACT RESID-alternate [] synonym: "chondroitin 6-sulfate (chondroitin sulfate C)" EXACT RESID-alternate [] synonym: "O-linked (Xyl...) (chondroitin sulfate)" EXACT UniProt-feature [] synonym: "poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine; poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-6-sulfate D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine" EXACT RESID-systematic [] xref: DiffAvg: "-1.01" xref: DiffFormula: "C 0 H -1 N 0 O 0" xref: DiffMono: "-1.007825" xref: Formula: "C 3 H 4 N 1 O 2" xref: MassAvg: "86.07" xref: MassMono: "86.024203" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] id: MOD:00214 name: dermatan 4-sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:2914936, PubMed:3472204, RESID:AA0209] subset: PSI-MOD_slim synonym: "beta-heparin" EXACT RESID-alternate [] synonym: "chondroitin sulfate B" EXACT RESID-alternate [] synonym: "O-linked (Xyl...) (dermatan sulfate)" EXACT UniProt-feature [] synonym: "poly[beta-1,4-L-idopyranuronosyl-alpha-1,3-(2-acetamido-2-deoxy-4-sulfate D-galactosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine" EXACT RESID-systematic [] xref: DiffAvg: "-1.01" xref: DiffFormula: "C 0 H -1 N 0 O 0" xref: DiffMono: "-1.007825" xref: Formula: "C 3 H 4 N 1 O 2" xref: MassAvg: "86.07" xref: MassMono: "86.024203" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] id: MOD:00215 name: heparan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:3472204, RESID:AA0210] subset: PSI-MOD_slim synonym: "heparin" EXACT RESID-alternate [] synonym: "heparitin sulfate" EXACT RESID-alternate [] synonym: "O-linked (Xyl...) (heparan sulfate)" EXACT UniProt-feature [] synonym: "poly[alpha-1,4-(2-sulfate D-glucopyranuronosyl)-beta-1,4-(2-sulfamino-2-deoxy-6-sulfate D-glucosyl)]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-serine" EXACT RESID-systematic [] xref: DiffAvg: "-1.01" xref: DiffFormula: "C 0 H -1 N 0 O 0" xref: DiffMono: "-1.007825" xref: Formula: "C 3 H 4 N 1 O 2" xref: MassAvg: "86.07" xref: MassMono: "86.024203" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] id: MOD:00216 name: N6-formyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-formyl-L-lysine." [PubMed:15799070, RESID:AA0211, UniMod:122] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-(formylamino)hexanoic acid" EXACT RESID-systematic [] synonym: "epsilon-formyllysine" EXACT RESID-alternate [] synonym: "Formyl" RELATED PSI-MS-label [] synonym: "Formylation" RELATED UniMod-description [] synonym: "N(zeta)-formyllysine" EXACT RESID-alternate [] synonym: "N6-formylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "N6-formyllysine" EXACT UniProt-feature [] synonym: "N6FoLys" EXACT PSI-MOD-short [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 H 0 N 0 O 1" xref: DiffMono: "27.994915" xref: Formula: "C 7 H 12 N 2 O 2" xref: MassAvg: "156.18" xref: MassMono: "156.089878" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00409 ! N-formylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00217 name: O4-arabinosyl-L-hydroxyproline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to O4-arabinosyl-L-hydroxyproline." [DeltaMass:0, PubMed:666730, PubMed:7852316, RESID:AA0212, UniMod:408] comment: secondary to RESID:AA0030; From DeltaMass: Average Mass: 147. subset: PSI-MOD_slim synonym: "(2S,4R)-4-(beta-L-arabinofuranosyloxy)pyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] synonym: "4-(beta-L-arabinofuranosyloxy)proline" EXACT RESID-alternate [] synonym: "4-Glycosyloxy- (pentosyl,C5) (of Proline)" EXACT DeltaMass-label [] synonym: "beta-arabinofuranosyl-4-hydroxyproline" EXACT RESID-alternate [] synonym: "Glycosyl" RELATED PSI-MS-label [] synonym: "glycosyl-L-hydroxyproline" RELATED UniMod-description [] synonym: "O4-glycosyl-hydroxyproline" EXACT RESID-alternate [] synonym: "OAra4HyPro" EXACT PSI-MOD-short [] xref: DiffAvg: "148.11" xref: DiffFormula: "C 5 H 8 N 0 O 5" xref: DiffMono: "148.037173" xref: Formula: "C 10 H 15 N 1 O 6" xref: MassAvg: "245.23" xref: MassMono: "245.089937" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00396 ! O-glycosylated residue is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00218 name: O-(phospho-5'-RNA)-L-serine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-serine residue and the 5'-end of RNA through a phosphodiester to form O4'-(phospho-5'-RNA)-L-serine." [PubMed:1705009, RESID:AA0213] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(5'-ribonucleic acid phosphonoxy)propanoic acid" EXACT RESID-systematic [] synonym: "O-(5'-phospho-RNA)-serine" EXACT UniProt-feature [] synonym: "O3-(phospho-5'-RNA)-L-serine" EXACT RESID-alternate [] synonym: "O3-L-serine 5'-RNA phosphodiester" EXACT RESID-alternate [] xref: DiffAvg: "78.97" xref: DiffFormula: "C 0 H 0 N 0 O 3 P 1" xref: DiffMono: "78.958505" xref: Formula: "C 3 H 5 N 1 O 5 P 1" xref: MassAvg: "166.05" xref: MassMono: "165.990534" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00751 ! ribonucleic acid linked residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00219 name: L-citrulline namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to L-citrulline." [DeltaMass:0, PubMed:2466844, RESID:AA0214, UniMod:7] comment: This modification is not the result of deamidation, instead the guanidino group is replaced with an ureido group. subset: PSI-MOD_slim synonym: "(S)-2-amino-5-(carbamoylamino)pentanoic acid" EXACT RESID-systematic [] synonym: "2-amino-5-(aminocarbonyl)aminopentanoic acid" EXACT RESID-alternate [] synonym: "alpha-amino-delta-ureidovaleric acid" EXACT RESID-alternate [] synonym: "Citrulline" EXACT DeltaMass-label [] synonym: "Citrulline" EXACT UniProt-feature [] synonym: "Deamidated" RELATED UniMod-interim [] synonym: "Deamidation" RELATED UniMod-description [] synonym: "delta-ureidonorvaline" EXACT RESID-alternate [] synonym: "N5-(aminocarbonyl)ornithine" EXACT RESID-alternate [] synonym: "N5-carbamoylornithine" EXACT RESID-alternate [] synonym: "N5-carbamylornithine" EXACT RESID-alternate [] xref: DiffAvg: "0.98" xref: DiffFormula: "C 0 H -1 N -1 O 1" xref: DiffMono: "0.984016" xref: Formula: "C 6 H 11 N 3 O 2" xref: MassAvg: "157.17" xref: MassMono: "157.085127" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00220 name: 4-hydroxy-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to a 4-hydroxy-L-arginine." [PubMed:10966817, PubMed:7650037, RESID:AA0215] subset: PSI-MOD_slim synonym: "(2S,4Xi)-2-amino-5-carbamimidamido-4-hydroxypentanoic acid" EXACT RESID-systematic [] synonym: "2-amino-5-guanidino-4-hydroxypentanoic acid" EXACT RESID-alternate [] synonym: "4-hydroxyarginine" EXACT UniProt-feature [] synonym: "4-hydroxylated L-arginine" EXACT PSI-MOD-alternate [] synonym: "4HyArg" EXACT PSI-MOD-short [] synonym: "C(gamma)-hydroxyarginine" EXACT RESID-alternate [] synonym: "gamma-hydroxyarginine" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 6 H 12 N 4 O 2" xref: MassAvg: "172.19" xref: MassMono: "172.096026" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00682 ! hydroxylated arginine [Term] id: MOD:00221 name: N-(L-isoaspartyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks L-aspartic acid and L-cysteine residues via an isopeptide bond to form N-(L-isoaspartyl)-L-cysteine." [PubMed:8286361, RESID:AA0216] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S)-2-amino-4-((R)-1-carboxy-2-sulfanylethyl)amino-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "2-(3-amino-3-carboxypropanoyl)amino-3-mercaptopropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-N4-(1-carboxy-2-mercaptoethyl)butanediamic acid" EXACT RESID-alternate [] synonym: "Isoaspartyl cysteine isopeptide (Cys-Asn)" EXACT UniProt-feature [] synonym: "N-beta-aspartylcysteine" EXACT RESID-alternate [] synonym: "N-isoaspartyl cysteine" EXACT RESID-alternate [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0 S 0" xref: DiffMono: "-17.026549" xref: Formula: "C 7 H 9 N 2 O 3 S 1" xref: MassAvg: "201.22" xref: MassMono: "201.033388" xref: Origin: "C, N" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00903 ! modified L-asparagine residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00222 name: 2'-alpha-mannosyl-L-tryptophan namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to 2'-alpha-mannosyl-L-tryptophan." [PubMed:15279557, PubMed:7547911, PubMed:7947762, RESID:AA0217, UniMod:41] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1H-2-alpha-mannopyranosyl-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "2'-tryptophan C-mannoside" EXACT RESID-alternate [] synonym: "C-linked (Man)" EXACT UniProt-feature [] synonym: "C2'ManTrp" EXACT PSI-MOD-short [] synonym: "Hex" RELATED PSI-MS-label [] synonym: "Hexose" RELATED UniMod-description [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 17 H 20 N 2 O 6" xref: MassAvg: "348.35" xref: MassMono: "348.132136" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00421 ! C-glycosylated residue is_a: MOD:00595 ! mannosylated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00223 name: N6-mureinyl-L-lysine namespace: PSI-MOD def: "modification from RESID" [PubMed:4261992, RESID:AA0218] subset: PSI-MOD_slim synonym: "N6-[(2R,6S)-2-(N-(N-mureinyl-(R)-alanyl)-(S)-glutamyl)amino-6-amino-6-carboxy-1-oxohex-1-yl]lysine" EXACT RESID-alternate [] synonym: "N6-murein peptidoglycan lysine" EXACT UniProt-feature [] xref: DiffAvg: "-1.01" xref: DiffFormula: "C 0 H -1 N 0 O 0" xref: DiffMono: "-1.007825" xref: Formula: "C 6 H 11 N 2 O 1" xref: MassAvg: "127.16" xref: MassMono: "127.087138" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01159 ! peptidoglycanated residue [Term] id: MOD:00224 name: 1-chondroitin sulfate-L-aspartic acid ester namespace: PSI-MOD def: "modification from RESID" [PubMed:1898736, RESID:AA0219] subset: PSI-MOD_slim synonym: "1-aspartic acid ester with 6-chondroitin 4-sulfate" EXACT RESID-alternate [] synonym: "Chondroitin 4-sulfate (covalent)" EXACT UniProt-feature [] synonym: "poly[beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate D-galactosyl)]beta-1,4-D-glucopyranuronosyl-beta-1,3-(2-acetamido-2-deoxy-4-sulfate-6-(1-L-aspartyl)-D-galactose)" EXACT RESID-alternate [] synonym: "protein-glycosaminoglycan-protein cross-link" EXACT RESID-alternate [] xref: DiffAvg: "441.36" xref: DiffFormula: "C 14 H 19 N 1 O 13 S 1" xref: DiffMono: "441.057711" xref: Formula: "C 18 H 25 N 2 O 17 S 1" xref: MassAvg: "573.46" xref: MassMono: "573.087393" xref: Origin: "D" xref: TermSpec: "C-term" is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00225 name: S-(6-FMN)-L-cysteine namespace: PSI-MOD def: "modification from RESID" [PubMed:10869173, PubMed:1551870, PubMed:620783, RESID:AA0220, UniMod:409] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[6-riboflavin 5'-dihydrogen phosphate]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "6-[S-cysteinyl]flavin mononucleotide" EXACT RESID-alternate [] synonym: "6-[S-cysteinyl]FMN" EXACT RESID-alternate [] synonym: "flavin mononucleotide" RELATED UniMod-description [] synonym: "FMNH" RELATED PSI-MS-label [] synonym: "S-6-FMN cysteine" EXACT UniProt-feature [] synonym: "S6FMNCys" EXACT PSI-MOD-short [] xref: DiffAvg: "454.33" xref: DiffFormula: "C 17 H 19 N 4 O 9 P 1 S 0" xref: DiffMono: "454.088965" xref: Formula: "C 20 H 24 N 5 O 10 P 1 S 1" xref: MassAvg: "557.47" xref: MassMono: "557.098150" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00896 ! FMN modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00226 name: 1'-(8alpha-FAD)-L-histidine namespace: PSI-MOD def: "modification from RESID" [DeltaMass:0, PubMed:10585424, PubMed:1396672, PubMed:4339951, PubMed:9261083, RESID:AA0221, UniMod:50] comment: From DeltaMass: Average Mass: 784 subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1-[8alpha riboflavin 5'-(trihydrogen diphosphate) 5'->5'-ester with adenosine]imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "8alpha-(N(epsilon)-histidyl)FAD" EXACT RESID-alternate [] synonym: "8alpha-(N1'-histidyl)FAD" EXACT RESID-alternate [] synonym: "8alpha-N3-histidyl FAD [misnomer]" RELATED RESID-misnomer [] synonym: "FAD" RELATED PSI-MS-label [] synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] synonym: "N theta and N pi-(8alpha-Flavin) (on Histidine)" EXACT DeltaMass-label [] synonym: "Ntele8aFADHis" EXACT PSI-MOD-short [] synonym: "tau-(8alpha-FAD)-histidine" EXACT RESID-alternate [] synonym: "tele-(8alpha-FAD)-histidine" EXACT RESID-alternate [] synonym: "Tele-8alpha-FAD histidine" EXACT UniProt-feature [] xref: DiffAvg: "783.53" xref: DiffFormula: "C 27 H 31 N 9 O 15 P 2" xref: DiffMono: "783.141485" xref: Formula: "C 33 H 38 N 12 O 16 P 2" xref: MassAvg: "920.67" xref: MassMono: "920.200396" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00895 ! FAD modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00227 name: omega-N-phospho-L-arginine namespace: PSI-MOD def: "modification from RESID" [PubMed:8300603, RESID:AA0222, UniMod:21] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-delta-phosphonoguanidinovaleric acid" EXACT RESID-alternate [] synonym: "N5-[imino(phosphonoamino)methyl]-L-ornithine" EXACT RESID-alternate [] synonym: "PhosArg" EXACT PSI-MOD-short [] synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phosphoarginine" EXACT UniProt-feature [] synonym: "Phosphorylation" RELATED UniMod-description [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 6 H 13 N 4 O 4 P 1" xref: MassAvg: "236.17" xref: MassMono: "236.067442" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00228 name: S-diphytanylglycerol diether-L-cysteine namespace: PSI-MOD def: "modification from RESID" [PubMed:7797461, PubMed:8195126, RESID:AA0223, UniMod:410] comment: incidental to RESID:AA0043 subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2,3-(3,7,11,15-tetramethylhexadecanyloxy)propyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "Archaeol" RELATED PSI-MS-label [] synonym: "S-(1-2',3'-phytanyl glycerol)cysteine" EXACT RESID-alternate [] synonym: "S-archaeol cysteine" EXACT UniProt-feature [] synonym: "S-archaeol cysteine" EXACT RESID-alternate [] synonym: "S-diphytanylglycerol diether" RELATED UniMod-description [] xref: DiffAvg: "635.14" xref: DiffFormula: "C 43 H 86 N 0 O 2 S 0" xref: DiffMono: "634.662782" xref: Formula: "C 46 H 91 N 1 O 3 S 1" xref: MassAvg: "738.28" xref: MassMono: "737.671967" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00229 name: alpha-1-microglobulin-Ig alpha complex chromophore namespace: PSI-MOD def: "modification from RESID" [PubMed:11058759, PubMed:11877257, PubMed:7506257, PubMed:7535251, RESID:AA0224] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "Multimeric 3-hydroxykynurenine chromophore (covalent)" EXACT UniProt-feature [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 6 H 8 N 2 O 2 S 2" xref: MassAvg: "204.27" xref: MassMono: "204.002720" xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00230 name: bis-L-cysteinyl bis-L-histidino diiron disulfide namespace: PSI-MOD def: "A protein modification that effectively converts three L-cysteine residues and an L-histidine residue to bis-L-cysteinyl bis-L-histidino diiron disulfide." [PubMed:2765515, PubMed:9651245, RESID:AA0225] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "di-mu-sulfido(bis-S-cysteinyliron)(bis-N3'-histidinoiron)" EXACT RESID-systematic [] synonym: "Rieske iron-sulfur cofactor" EXACT RESID-alternate [] xref: DiffAvg: "171.79" xref: DiffFormula: "C 0 Fe 2 H -4 N 0 O 0 S 2" xref: DiffMono: "171.782717" xref: Formula: "C 18 Fe 2 H 20 N 8 O 4 S 4" xref: MassAvg: "652.35" xref: MassMono: "651.918910" xref: Origin: "C, C, H, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00231 name: hexakis-L-cysteinyl hexairon hexasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:1311311, PubMed:1318833, RESID:AA0226] comment: Cross-link 6. subset: PSI-MOD_slim synonym: "hexa-mu3-sulfidohexakis(S-cysteinyliron)" EXACT RESID-systematic [] synonym: "prismane iron-sulfur cofactor" EXACT RESID-alternate [] xref: DiffAvg: "521.41" xref: DiffFormula: "C 0 Fe 6 H -6 N 0 O 0 S 6" xref: DiffMono: "521.395101" xref: Formula: "C 18 Fe 6 H 24 N 6 O 6 S 12" xref: MassAvg: "1140.27" xref: MassMono: "1139.450209" xref: Origin: "C, C, C, C, C, C" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00232 name: N6-(phospho-5'-adenosine)-L-lysine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-lysine residue and 5'-phosphoadenosine through a phosphoramide ester bond to form N6-(phospho-5'-adenosine)-L-lysine." [DeltaMass:316, PubMed:3882425, PubMed:4944632, RESID:AA0227, UniMod:405] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-(5'-adenosine phosphonamino)hexanoic acid" EXACT RESID-systematic [] synonym: "5'-adenylic-N6-L-lysine" EXACT RESID-alternate [] synonym: "AMP binding site" RELATED UniMod-description [] synonym: "AMP Lysyl" EXACT DeltaMass-label [] synonym: "epsilon-5'-adenylic-L-lysine" EXACT RESID-alternate [] synonym: "L-lysine monoanhydride with 5'-adenylic acid" EXACT RESID-alternate [] synonym: "N(zeta)-5'-adenylic-L-lysine" EXACT RESID-alternate [] synonym: "N6-L-lysine 5'-adenosine phosphoramidester" EXACT RESID-alternate [] synonym: "Phosphoadenosine" RELATED PSI-MS-label [] xref: DiffAvg: "329.21" xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1" xref: DiffMono: "329.052520" xref: Formula: "C 16 H 24 N 7 O 7 P 1" xref: MassAvg: "457.38" xref: MassMono: "457.147483" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01165 ! adenylated residue [Term] id: MOD:00233 name: N6-(phospho-5'-guanosine)-L-lysine namespace: PSI-MOD def: "modification from RESID" [DeltaMass:304, PubMed:6092377, PubMed:6264433, RESID:AA0228, UniMod:413] comment: From DeltaMass: Average Mass: 345 Formula:C10H12O5N7P1 Monoisotopic Mass Change:345.047 Average Mass Change:345.209 References:PE Sciex subset: PSI-MOD_slim synonym: "(S)-2-amino-6-(5'-guanosine phosphonamino)hexanoic acid" EXACT RESID-systematic [] synonym: "5'-guanylic-N6-L-lysine" EXACT RESID-alternate [] synonym: "5'phos Guanosyl" EXACT DeltaMass-label [] synonym: "epsilon-5'-guanylic-L-lysine" EXACT RESID-alternate [] synonym: "L-lysine monoanhydride with 5'-guanylic acid" EXACT RESID-alternate [] synonym: "lysine guanosine-5'-monophosphate" EXACT RESID-alternate [] synonym: "N(zeta)-5'-guanylic-lysine" EXACT RESID-alternate [] synonym: "N6-L-lysine 5'-guanosine phosphoramidester" EXACT RESID-alternate [] synonym: "phospho-guanosine" RELATED UniMod-description [] synonym: "Phosphoguanosine" RELATED PSI-MS-label [] xref: DiffAvg: "345.21" xref: DiffFormula: "C 10 H 12 N 5 O 7 P 1" xref: DiffMono: "345.047434" xref: Formula: "C 16 H 24 N 7 O 8 P 1" xref: MassAvg: "473.38" xref: MassMono: "473.142397" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01163 ! guanylated residue [Term] id: MOD:00234 name: L-cysteine glutathione disulfide namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-glutathionyl-L-cysteine." [ChEBI:21264, DeltaMass:0, PubMed:3083866, PubMed:8344916, RESID:AA0229, UniMod:55] comment: From DeltaMass: Average Mass: 305 subset: PSI-MOD_slim synonym: "(2S)-2-amino-3-((2S)-2-((4R)-4-amino-4-carboxyl-1-oxobutyl)amino-3-(carboxylmethyl)amino-3-oxo-propyl)dithio-propanoic acid" EXACT RESID-systematic [] synonym: "cysteinyl glutathione" EXACT RESID-alternate [] synonym: "Glutathionation" EXACT DeltaMass-label [] synonym: "Glutathione" RELATED PSI-MS-label [] synonym: "glutathione disulfide" RELATED UniMod-description [] synonym: "L-gamma-glutamyl-L-cysteinyl-glycine (2-1')-disulfide with L-cysteine" EXACT RESID-alternate [] synonym: "N-(N-gamma-glutamyl-cystinyl)-glycine" EXACT RESID-alternate [] synonym: "S-glutathionyl cysteine" EXACT UniProt-feature [] xref: DiffAvg: "305.31" xref: DiffFormula: "C 10 H 15 N 3 O 6 S 1" xref: DiffMono: "305.068156" xref: Formula: "C 13 H 20 N 4 O 7 S 2" xref: MassAvg: "408.45" xref: MassMono: "408.077341" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00235 name: S-nitrosyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-nitrosyl-L-cysteine." [PubMed:10442087, PubMed:11562475, PubMed:15688001, PubMed:8626764, PubMed:8637569, RESID:AA0230, UniMod:275] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-nitrososulfanyl-propanoic acid" EXACT RESID-systematic [] synonym: "L-cysteine nitrite ester" EXACT RESID-alternate [] synonym: "Nitrosyl" RELATED PSI-MS-label [] synonym: "S-nitrosocysteine" EXACT UniProt-feature [] synonym: "S-nitrosocysteine" EXACT RESID-alternate [] synonym: "S-nitrosylation" RELATED UniMod-description [] synonym: "SNOCys" EXACT PSI-MOD-short [] xref: DiffAvg: "29.00" xref: DiffFormula: "C 0 H -1 N 1 O 1 S 0" xref: DiffMono: "28.990164" xref: Formula: "C 3 H 4 N 2 O 2 S 1" xref: MassAvg: "132.14" xref: MassMono: "131.999348" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00236 name: N4-(ADP-ribosyl)-L-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to N4-(ADP-ribosyl)-L-asparagine." [PubMed:15842200, PubMed:2498316, RESID:AA0231, UniMod:213] subset: PSI-MOD_slim synonym: "(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "ADP Ribose addition" RELATED UniMod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "ADP-ribosylasparagine" EXACT UniProt-feature [] synonym: "N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine" EXACT RESID-alternate [] synonym: "N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT RESID-alternate [] xref: DiffAvg: "541.30" xref: DiffFormula: "C 15 H 21 N 5 O 13 P 2" xref: DiffMono: "541.061109" xref: Formula: "C 19 H 27 N 7 O 15 P 2" xref: MassAvg: "655.40" xref: MassMono: "655.104036" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00237 name: L-beta-methylthioaspartic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to L-beta-methylthioaspartic acid." [DeltaMass:61, PubMed:15473684, PubMed:8844851, RESID:AA0232, UniMod:39] subset: PSI-MOD_slim synonym: "(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid" EXACT RESID-systematic [] synonym: "3-carboxy-S-methyl-cysteine" EXACT RESID-alternate [] synonym: "3-methylthio-aspartic acid" EXACT RESID-alternate [] synonym: "3-methylthioaspartic acid" EXACT UniProt-feature [] synonym: "beta-Methylthio-aspartic acid" EXACT DeltaMass-label [] synonym: "beta-methylthio-aspartic acid" EXACT RESID-alternate [] synonym: "Beta-methylthiolation" RELATED UniMod-description [] synonym: "Methylthio" RELATED UniMod-interim [] xref: DiffAvg: "46.09" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 1" xref: DiffMono: "45.987721" xref: Formula: "C 5 H 7 N 1 O 3 S 1" xref: MassAvg: "161.18" xref: MassMono: "161.014664" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01153 ! methylthiolated residue [Term] id: MOD:00238 name: 5'-(N6-L-lysine)-L-topaquinone namespace: PSI-MOD def: "modification from RESID" [PubMed:8688089, RESID:AA0233] comment: Cross-link 2; secondary to RESID:AA0147. subset: PSI-MOD_slim synonym: "1-[(S)-5-amino-5-carboxypentyl]amino-2-[(S)-2-amino-2-carboxyethyl]-2,6-cyclohexadien-4,5-dione" EXACT RESID-systematic [] synonym: "5'-(L-lysine)-L-tyrosylquinone" EXACT RESID-alternate [] synonym: "Lysine tyrosylquinone (Lys-Tyr)" EXACT UniProt-feature [] synonym: "lysyl oxidase cofactor" EXACT RESID-alternate [] xref: DiffAvg: "11.97" xref: DiffFormula: "C 0 H -4 N 0 O 1" xref: DiffMono: "11.963614" xref: Formula: "C 15 H 17 N 3 O 4" xref: MassAvg: "303.31" xref: MassMono: "303.121906" xref: Origin: "K, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00239 name: S-methyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-methyl-L-cysteine." [PubMed:10660523, PubMed:11875433, PubMed:1339288, RESID:AA0234, UniMod:34] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(methylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "L-3-(methylthio)alanine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "S-methylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "S-methylcysteine" EXACT UniProt-feature [] synonym: "SMeCys" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 0" xref: DiffMono: "14.015650" xref: Formula: "C 4 H 7 N 1 O 1 S 1" xref: MassAvg: "117.17" xref: MassMono: "117.024835" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00654 ! S-methylated residue is_a: MOD:00660 ! methylated cysteine [Term] id: MOD:00240 name: 4-hydroxy-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to 4-hydroxy-L-lysine." [PubMed:4005040, RESID:AA0235] subset: PSI-MOD_slim synonym: "(2S,4R)-2,6-diamino-4-hydroxyhexanoic acid" EXACT RESID-systematic [] synonym: "4-hydroxylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "4HyLys" EXACT PSI-MOD-short [] synonym: "alpha,epsilon-diamino-gamma-hydroxycaproic acid" EXACT RESID-alternate [] synonym: "L-threo-gamma-hydroxylysine" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 6 H 12 N 2 O 2" xref: MassAvg: "144.17" xref: MassMono: "144.089878" xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:01047 ! monohydroxylated lysine [Term] id: MOD:00241 name: N4-hydroxymethyl-L-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to N4-hydroxymethyl-L-asparagine." [RESID:AA0236, UniMod:414] comment: This modification has not been observed to occur naturally. subset: PSI-MOD_slim synonym: "(S)-2-amino-N4-hydroxymethylbutanediamic acid" EXACT RESID-systematic [] synonym: "beta-hydroxymethylasparagine" EXACT RESID-alternate [] synonym: "Hydroxymethyl" RELATED PSI-MS-label [] synonym: "hydroxymethyl" RELATED UniMod-description [] synonym: "N(gamma)-hydroxymethylasparagine" EXACT RESID-alternate [] synonym: "N4-hydroxymethylasparagine" EXACT RESID-alternate [] xref: DiffAvg: "30.03" xref: DiffFormula: "C 1 H 2 N 0 O 1" xref: DiffMono: "30.010565" xref: Formula: "C 5 H 8 N 2 O 3" xref: MassAvg: "144.13" xref: MassMono: "144.053492" xref: Origin: "N" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00242 name: O-(ADP-ribosyl)-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-(ADP-ribosyl)-L-serine." [PubMed:15842200, PubMed:3141412, RESID:AA0237, UniMod:213] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid" EXACT RESID-systematic [] synonym: "ADP Ribose addition" RELATED UniMod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "ADP-ribosylserine" EXACT UniProt-feature [] synonym: "O3-(ADP-ribosyl)-L-serine" EXACT RESID-alternate [] synonym: "O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine" EXACT RESID-alternate [] synonym: "O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)" EXACT RESID-alternate [] xref: DiffAvg: "541.30" xref: DiffFormula: "C 15 H 21 N 5 O 13 P 2" xref: DiffMono: "541.061109" xref: Formula: "C 18 H 26 N 6 O 15 P 2" xref: MassAvg: "628.38" xref: MassMono: "628.093137" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00243 name: L-cysteine oxazole-4-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and an L-serine residue to form L-cysteine oxazole-4-carboxylic acid." [PubMed:8183941, PubMed:8895467, RESID:AA0238] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-(1-amino-2-sulfanylethyl)-4-oxazolecarboxylic acid" EXACT RESID-systematic [] synonym: "Oxazole-4-carboxylic acid (Cys-Ser)" EXACT UniProt-feature [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1 S 0" xref: DiffMono: "-20.026215" xref: Formula: "C 6 H 6 N 2 O 2 S 1" xref: MassAvg: "170.19" xref: MassMono: "170.014998" xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00244 name: L-cysteine oxazoline-4-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and an L-serine residue to form L-cysteine oxazoline-4-carboxylic acid." [PubMed:1880060, RESID:AA0239] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S)-2-((R)-1-amino-2-sulfanylethyl)-4-oxazolinecarboxylic acid" EXACT RESID-systematic [] synonym: "Oxazoline-4-carboxylic acid (Cys-Ser)" EXACT UniProt-feature [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 6 H 8 N 2 O 2 S 1" xref: MassAvg: "172.20" xref: MassMono: "172.030649" xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00245 name: glycine oxazole-4-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively crosslinks a glycine residue and an L-serine residue to form glycine oxazole-4-carboxylic acid." [PubMed:8183941, PubMed:8895467, RESID:AA0240] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "2-aminomethyl-4-oxazolecarboxylic acid" EXACT RESID-systematic [] synonym: "Oxazole-4-carboxylic acid (Gly-Ser)" EXACT UniProt-feature [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1" xref: DiffMono: "-20.026215" xref: Formula: "C 5 H 4 N 2 O 2" xref: MassAvg: "124.10" xref: MassMono: "124.027277" xref: Origin: "G, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00246 name: glycine thiazole-4-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and a glycine residue to form glycine thiazole-4-carboxylic acid." [ChEBI:21276, PubMed:8183941, PubMed:8895467, RESID:AA0241] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "2-aminomethyl-4-thiazolecarboxylic acid" EXACT RESID-systematic [] synonym: "Thiazole-4-carboxylic acid (Gly-Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1 S 0" xref: DiffMono: "-20.026215" xref: Formula: "C 5 H 4 N 2 O 1 S 1" xref: MassAvg: "140.16" xref: MassMono: "140.004434" xref: Origin: "C, G" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues [Term] id: MOD:00247 name: L-serine thiazole-4-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and an L-serine residue to form L-serine thiazole-4-carboxylic acid." [PubMed:8183941, PubMed:8895467, RESID:AA0242] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-(1-amino-2-hydroxyethyl)-4-thiazolecarboxylic acid" EXACT RESID-systematic [] synonym: "Thiazole-4-carboxylic acid (Ser-Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1 S 0" xref: DiffMono: "-20.026215" xref: Formula: "C 6 H 6 N 2 O 2 S 1" xref: MassAvg: "170.19" xref: MassMono: "170.014998" xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues [Term] id: MOD:00248 name: L-phenylalanine thiazole-4-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and an L-phenylalanine residue to form L-phenylalanine thiazole-4-carboxylic acid." [PubMed:1880060, RESID:AA0243] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-(1-amino-2-phenylethyl)-4-thiazolecarboxylic acid" EXACT RESID-systematic [] synonym: "Thiazole-4-carboxylic acid (Phe-Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1 S 0" xref: DiffMono: "-20.026215" xref: Formula: "C 12 H 10 N 2 O 1 S 1" xref: MassAvg: "230.29" xref: MassMono: "230.051384" xref: Origin: "C, F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00914 ! modified L-phenylalanine residue is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues [Term] id: MOD:00249 name: L-cysteine thiazole-4-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively crosslinks two L-cysteine residues to form L-cysteine thiazole-4-carboxylic acid." [PubMed:1880060, RESID:AA0244] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S)-2-(1-amino-2-sulfanylethyl)-4-thiazolecarboxylic acid" EXACT RESID-systematic [] synonym: "Thiazole-4-carboxylic acid (Cys-Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1 S 0" xref: DiffMono: "-20.026215" xref: Formula: "C 6 H 6 N 2 O 1 S 2" xref: MassAvg: "186.25" xref: MassMono: "185.992155" xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues [Term] id: MOD:00250 name: L-lysine thiazole-4-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-cysteine residue and an L-lysine residue to form L-lysine thiazole-4-carboxylic acid." [PubMed:1880060, RESID:AA0245] comment: Cross-link 2. Lysine is now thought not to be encoded in the peptide sequence modified to produce GE2270. See RESID:AA0470. subset: PSI-MOD_slim synonym: "(R)-2-(1,5-diaminopentyl)-4-thiazolecarboxylic acid" EXACT RESID-systematic [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1 S 0" xref: DiffMono: "-20.026215" xref: Formula: "C 9 H 13 N 3 O 1 S 1" xref: MassAvg: "211.28" xref: MassMono: "211.077933" xref: Origin: "C, K" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01420 ! thiazole/thiazoline ring croslinked residues [Term] id: MOD:00251 name: O-(phospho-5'-DNA)-L-serine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-serine residue and the 5'-end of DNA through a phosphodiester bond to form O-(phospho-5'-DNA)-L-serine." [PubMed:7142163, PubMed:7265205, RESID:AA0246] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(5'-deoxyribonucleic acid phosphonoxy)propanoic acid" EXACT RESID-systematic [] synonym: "O-(5'-phospho-DNA)-serine" EXACT UniProt-feature [] synonym: "O3-(phospho-5'-DNA)-L-serine" EXACT RESID-alternate [] synonym: "O3-L-serine 5'-DNA phosphodiester" EXACT RESID-alternate [] xref: DiffAvg: "78.97" xref: DiffFormula: "C 0 H 0 N 0 O 3 P 1" xref: DiffMono: "78.958505" xref: Formula: "C 3 H 5 N 1 O 5 P 1" xref: MassAvg: "166.05" xref: MassMono: "165.990534" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00750 ! deoxyribonucleic acid linked residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00252 name: keratan sulfate D-glucuronosyl-D-galactosyl-D-galactosyl-D-xylosyl-L-threonine namespace: PSI-MOD def: "modification from RESID" [PubMed:1417734, PubMed:3472204, RESID:AA0247] subset: PSI-MOD_slim synonym: "keratosulfate" EXACT RESID-alternate [] synonym: "O-linked (Xyl...) (keratan sulfate)" EXACT UniProt-feature [] synonym: "poly[beta-1,4-(2-acetamido-2-deoxy-6-sulfate D-glucosyl)-beta-1,3-D-galactosyl]-beta-1,4-D-glucopyranuronosyl-beta-1,3-D-galactosyl-beta-1,3-D-galactosyl-beta-1,4-D-xylosyl-beta-1,3-L-threonine" EXACT RESID-systematic [] xref: DiffAvg: "-1.01" xref: DiffFormula: "C 0 H -1 N 0 O 0" xref: DiffMono: "-1.007825" xref: Formula: "C 4 H 6 N 1 O 2" xref: MassAvg: "100.10" xref: MassMono: "100.039853" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00005 ! O-glycosyl-L-threonine [Term] id: MOD:00254 name: O4'-(phospho-5'-RNA)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-tyrosine residue and the 5'-end of RNA through a phosphodiester to form O4'-(phospho-5'-RNA)-L-tyrosine." [PubMed:1702164, PubMed:209034, PubMed:217003, PubMed:6264310, RESID:AA0249] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[4-(5'-ribonucleic acid phosphonoxy)phenyl]propanoic acid" EXACT RESID-systematic [] synonym: "O-(5'-phospho-RNA)-tyrosine" EXACT UniProt-feature [] synonym: "O4'-L-tyrosine 5'-RNA phosphodiester" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 9 H 10 N 1 O 5 P 1" xref: MassAvg: "243.15" xref: MassMono: "243.029659" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00751 ! ribonucleic acid linked residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00255 name: 3-(3'-L-histidyl)-L-tyrosine namespace: PSI-MOD def: "modification from RESID" [PubMed:9144772, RESID:AA0250] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-[3-((S)-2-amino-2-carboxy-1-(4-hydoxyphenyl)ethyl)imidazol-4-yl]propanoic acid" EXACT RESID-systematic [] synonym: "3'-histidyl-3-tyrosine (His-Tyr)" EXACT UniProt-feature [] synonym: "3-(N3'-histidyl)tyrosine" EXACT RESID-alternate [] synonym: "3-(pi-histidyl)tyrosine" EXACT RESID-alternate [] synonym: "3-(pros-histidyl)tyrosine" EXACT RESID-alternate [] synonym: "beta-(N(delta)-histidyl)tyrosine" EXACT RESID-alternate [] synonym: "beta-(N3'-histidyl)tyrosine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" xref: Formula: "C 15 H 14 N 4 O 3" xref: MassAvg: "298.30" xref: MassMono: "298.106590" xref: Origin: "H, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00256 name: L-methionine sulfone namespace: PSI-MOD def: "A protein modification that dioxygenates an L-methionine residue to L-methionine sulfone." [DeltaMass:205, PubMed:12686488, PubMed:7786407, PubMed:7791219, PubMed:9252331, RESID:AA0251, UniMod:425] comment: DeltaMass gives the formula C 5 H 9 N 3 O 1 S 1 with mass 163 subset: PSI-MOD_slim synonym: "(S)-2-amino-4-(methylsulfonyl)butanoic acid" EXACT RESID-systematic [] synonym: "dihydroxy" RELATED UniMod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "L-methionine S,S-dioxide" EXACT RESID-alternate [] synonym: "Methionine sulfone" EXACT UniProt-feature [] synonym: "MethionylSulphone" EXACT DeltaMass-label [] synonym: "MetO2" EXACT PSI-MOD-short [] synonym: "Oxidation of Methionine (to Sulphone)" EXACT DeltaMass-label [] synonym: "S,S-dioxymethionine" EXACT RESID-alternate [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2 S 0" xref: DiffMono: "31.989829" xref: Formula: "C 5 H 9 N 1 O 3 S 1" xref: MassAvg: "163.19" xref: MassMono: "163.030314" xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00709 ! sulfur oxygenated L-methionine [Term] id: MOD:00257 name: dipyrrolylmethanemethyl-L-cysteine namespace: PSI-MOD def: "modification from RESID" [PubMed:3042456, PubMed:3196304, PubMed:3421931, PubMed:8727319, RESID:AA0252, UniMod:416] subset: PSI-MOD_slim synonym: "3-[5-(3-acetic acid-4-propanoic acid-1-pyrrol-2-yl)methyl-3-acetic acid-4-propanoic acid-1-pyrrol-2-yl]methylthio-2-aminopropanoic acid" EXACT RESID-alternate [] synonym: "3-[5-[4-(2-carboxy)ethyl-3-carboxymethyl-1-pyrrol-2-yl]methyl-4-(2-carboxy)ethyl-3-carboxymethyl-1-pyrrol-2-yl]methylthio-2-aminopropanoic acid" EXACT RESID-systematic [] synonym: "dipyrrole cofactor" EXACT RESID-alternate [] synonym: "Dipyrrolylmethanemethyl" RELATED PSI-MS-label [] synonym: "dipyrrolylmethanemethyl" RELATED UniMod-description [] synonym: "dipyrrolylmethyl-L-cysteine" EXACT RESID-alternate [] synonym: "dipyrromethane cofactor" EXACT RESID-alternate [] synonym: "pyrromethane cofactor" EXACT RESID-alternate [] synonym: "Pyrromethane cofactor (covalent)" EXACT UniProt-feature [] xref: DiffAvg: "418.40" xref: DiffFormula: "C 20 H 22 N 2 O 8 S 0" xref: DiffMono: "418.137616" xref: Formula: "C 23 H 27 N 3 O 9 S 1" xref: MassAvg: "521.54" xref: MassMono: "521.146800" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00258 name: S-(2-aminovinyl)-3-methyl-D-cysteine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-threonine residue by a thioether bond to form S-(2-aminovinyl)-3-methyl-D-cysteine." [PubMed:9119018, RESID:AA0253] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S,3S)-2-amino-3-[((Z)-2-aminovinyl)sulfanyl]butanoic acid" EXACT RESID-systematic [] synonym: "decarboxylated methyllanthionine" EXACT RESID-alternate [] synonym: "S-(2-aminovinyl)-3-methyl-D-cysteine (Thr-Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-64.04" xref: DiffFormula: "C -1 H -4 N 0 O -3 S 0" xref: DiffMono: "-64.016044" xref: Formula: "C 6 H 9 N 2 O 1 S 1" xref: MassAvg: "157.21" xref: MassMono: "157.043559" xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00259 name: O4'-(phospho-5'-DNA)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-tyrosine residue and the 5'-end of DNA through a phosphodiester bond to form O4'-(phospho-5'-DNA)-L-tyrosine." [PubMed:1861973, PubMed:2940511, PubMed:3684578, RESID:AA0254] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[4-(5'-deoxyribonucleic acid phosphonoxy)phenyl]propanoic acid" EXACT RESID-systematic [] synonym: "O-(5'-phospho-DNA)-tyrosine" EXACT UniProt-feature [] synonym: "O4'-L-tyrosine 5'-DNA phosphodiester" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 9 H 10 N 1 O 5 P 1" xref: MassAvg: "243.15" xref: MassMono: "243.029659" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00750 ! deoxyribonucleic acid linked residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00260 name: O-(phospho-5'-DNA)-L-threonine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-threonine residue and the 5'-end of DNA through a phosphodiester bond to form O-(phospho-5'-DNA)-L-threonine." [PubMed:3081736, RESID:AA0255] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(5'-deoxyribonucleic acid phosphonoxy)butanoic acid" EXACT RESID-systematic [] synonym: "O3-(phospho-5'-DNA)-L-threonine" EXACT RESID-alternate [] synonym: "O3-L-threonine 5'-DNA phosphodiester" EXACT RESID-alternate [] xref: DiffAvg: "78.97" xref: DiffFormula: "C 0 H 0 N 0 O 3 P 1" xref: DiffMono: "78.958505" xref: Formula: "C 4 H 7 N 1 O 5 P 1" xref: MassAvg: "180.08" xref: MassMono: "180.006184" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00750 ! deoxyribonucleic acid linked residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00261 name: O4'-(phospho-5'-uridine)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-tyrosine residue and 5'-phosphouridine through a phosphodiester bond to form O4'-(phospho-5'-uridine)-L-tyrosine." [DeltaMass:0, PubMed:11467524, PubMed:2885322, RESID:AA0256, UniMod:417] comment: From DeltaMass: Average Mass: 306. subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[4-(5'-uridine phosphonoxy)phenyl]propanoic acid" EXACT RESID-systematic [] synonym: "5'-uridylic-O-tyrosine" EXACT RESID-alternate [] synonym: "hydrogen 5'-uridylate tyrosine ester" EXACT RESID-alternate [] synonym: "O-UMP-tyrosine" EXACT UniProt-feature [] synonym: "O-Uridinylylation (of Tyrosine)" EXACT DeltaMass-label [] synonym: "O4'-L-tyrosine 5'-uridine phosphodiester" EXACT RESID-alternate [] synonym: "PhosphoUridine" RELATED PSI-MS-label [] synonym: "uridine phosphodiester" RELATED UniMod-description [] xref: DiffAvg: "306.17" xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1" xref: DiffMono: "306.025302" xref: Formula: "C 18 H 20 N 3 O 10 P 1" xref: MassAvg: "469.34" xref: MassMono: "469.088630" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:01166 ! uridylated residue [Term] id: MOD:00262 name: N-(L-glutamyl)-L-tyrosine namespace: PSI-MOD def: "modification from RESID" [ChEBI:21477, PubMed:6387372, PubMed:8093886, RESID:AA0257] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S,S)-2-(2-aminopentanedio-1-yl)amino-3-(4-hydoxyphenyl)propanoic acid" EXACT RESID-systematic [] xref: DiffAvg: "-17.01" xref: DiffFormula: "C 0 H -1 N 0 O -1" xref: DiffMono: "-17.002740" xref: Formula: "C 14 H 16 N 2 O 5" xref: MassAvg: "292.29" xref: MassMono: "292.105922" xref: Origin: "E, Y" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00263 name: S-phycoviolobilin-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycoviolobilin." [PubMed:2106585, PubMed:3208761, RESID:AA0258, UniMod:387] subset: PSI-MOD_slim synonym: "(4S)-3-[(1R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-18-ethyl-4,5-dihydro-2,7,13,17-tetramethyl-(21H,22H,24H)-biladiene-bc-1,19-dione" EXACT RESID-systematic [] synonym: "cryptobiliviolin" EXACT RESID-alternate [] synonym: "cryptoviolin" EXACT RESID-alternate [] synonym: "cryptoviolobilin" EXACT RESID-alternate [] synonym: "Phycocyanobilin" RELATED PSI-MS-label [] synonym: "phycocyanobilin" RELATED UniMod-description [] synonym: "S-phycobiliviolin-L-cysteine" EXACT RESID-alternate [] xref: DiffAvg: "586.68" xref: DiffFormula: "C 33 H 38 N 4 O 6 S 0" xref: DiffMono: "586.279135" xref: Formula: "C 36 H 43 N 5 O 7 S 1" xref: MassAvg: "689.82" xref: MassMono: "689.288320" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00264 name: phycoerythrobilin-bis-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between two cysteine residues and the tetrapyrrole compound phycoerythrobilin." [PubMed:3208761, PubMed:3838747, RESID:AA0259] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S,3R,16R)-3,18-bis-[(R)-1-(((2R)-2-amino-2-carboxy)ethylsulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-2,3,15,16-tetrahydrobilin-1,19(21H,22H,24H)-dione" EXACT RESID-systematic [] synonym: "3,18-bis-[1-((2-amino-2-carboxy)ethylsulfanyl)ethyl]-2,3,15,16-tetrahydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-biladiene-ab-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "phycoerythrobilin biscysteine adduct" EXACT RESID-alternate [] xref: DiffAvg: "586.68" xref: DiffFormula: "C 33 H 38 N 4 O 6 S 0" xref: DiffMono: "586.279135" xref: Formula: "C 39 H 48 N 6 O 8 S 2" xref: MassAvg: "792.96" xref: MassMono: "792.297505" xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00265 name: phycourobilin-bis-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between two cysteine residues and the tetrapyrrole compound phycourobilin." [PubMed:3208761, PubMed:3838665, PubMed:3838747, PubMed:8876649, RESID:AA0260] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "3,18-bis(1-[(R)-2-amino-2-carboxyethyl]sulfanylethyl)-2,7,13,17-tetramethyl-1,19-dioxo-4,5,15,16-tetrahydro-(21H,22H,24H)-bilene-b-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "3,18-bis(1-[(R)-2-amino-2-carboxyethyl]sulfanylethyl)-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-4,5,15,16-tetrahydro-(21H,22H,24H)-bilene-b-1,19(4H,16H)-dione" EXACT RESID-systematic [] synonym: "phycourobilin biscysteine adduct" EXACT RESID-alternate [] xref: DiffAvg: "586.68" xref: DiffFormula: "C 33 H 38 N 4 O 6 S 0" xref: DiffMono: "586.279135" xref: Formula: "C 39 H 48 N 6 O 8 S 2" xref: MassAvg: "792.96" xref: MassMono: "792.297505" xref: Origin: "C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00266 name: N-L-glutamyl-poly-L-glutamic acid namespace: PSI-MOD def: "modification from RESID" [PubMed:2570347, PubMed:328274, RESID:AA0261] subset: PSI-MOD_slim xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 10 H 15 N 2 O 7" xref: MassAvg: "275.24" xref: MassMono: "275.087926" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00267 name: L-cysteine sulfinic acid namespace: PSI-MOD def: "A protein modification that effectively dioxygenates an L-cysteine residue to L-cysteine sulfinic acid." [ChEBI:16345, PubMed:12686488, PubMed:9252331, PubMed:9586994, RESID:AA0262, UniMod:425] comment: "Hyun Ae Woo, et. al., Science 300 (5619), 653-656" subset: PSI-MOD_slim synonym: "(R)-2-amino-2-carboxyethanesulfinic acid" EXACT RESID-systematic [] synonym: "2-amino-3-sulfinopropanoic acid" EXACT RESID-alternate [] synonym: "3-sulfinoalanine" EXACT RESID-alternate [] synonym: "CysO2H" EXACT PSI-MOD-short [] synonym: "Cysteine sulfinic acid (-SO2H)" EXACT UniProt-feature [] synonym: "cysteine-S,S-dioxide" EXACT RESID-alternate [] synonym: "dihydroxy" RELATED UniMod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "S-cysteinesulfinic acid" EXACT RESID-alternate [] synonym: "S-sulfinocysteine" EXACT RESID-alternate [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2 S 0" xref: DiffMono: "31.989829" xref: Formula: "C 3 H 5 N 1 O 3 S 1" xref: MassAvg: "135.14" xref: MassMono: "134.999014" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00708 ! sulfur oxygenated L-cysteine [Term] id: MOD:00268 name: L-3',4',5'-trihydroxyphenylalanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to L-3',4',5'-trihydroxyphenylalanine." [DeltaMass:0, PubMed:12686488, PubMed:12771378, PubMed:8554314, PubMed:9252331, PubMed:9434739, RESID:AA0263, UniMod:425] comment: From DeltaMass: Average Mass: 32 subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(3,4,5-trihydroxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "3,4,6-Trihydroxy-Phenylalanine (from Tyrosine) (TOPA)" EXACT DeltaMass-label [] synonym: "35Hy2Tyr" EXACT PSI-MOD-short [] synonym: "dihydroxy" RELATED UniMod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "L-3,4,5-TOPA" EXACT RESID-alternate [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2" xref: DiffMono: "31.989829" xref: Formula: "C 9 H 9 N 1 O 4" xref: MassAvg: "195.17" xref: MassMono: "195.053158" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00707 ! hydroxylated tyrosine [Term] id: MOD:00269 name: O-(sn-1-glycerophosphoryl)-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:8645220, RESID:AA0264, UniMod:419] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[(Xi)-2,3-dihydroxypropyl]phosphonoxypropanoic acid" EXACT RESID-systematic [] synonym: "alpha-glycerophosphoryl serine" EXACT RESID-alternate [] synonym: "Glycerophospho" RELATED PSI-MS-label [] synonym: "glycerophospho" RELATED UniMod-description [] synonym: "glycerophosphoserine" EXACT RESID-alternate [] synonym: "O-(sn-1-glycerophosphoryl)serine" EXACT UniProt-feature [] synonym: "O3-(sn-1-glycerophosphoryl)-L-serine" EXACT RESID-alternate [] synonym: "O3-2,3-dihydroxypropyl hydrogen phosphate-L-serine ester" EXACT RESID-alternate [] synonym: "O3-L-serine glyceryl-1-phosphodiester" EXACT RESID-alternate [] xref: DiffAvg: "154.06" xref: DiffFormula: "C 3 H 7 N 0 O 5 P 1" xref: DiffMono: "154.003110" xref: Formula: "C 6 H 12 N 1 O 7 P 1" xref: MassAvg: "241.14" xref: MassMono: "241.035138" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00270 name: 1-thioglycine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to 1-thioglycine." [PubMed:11463785, PubMed:9367957, RESID:AA0265, UniMod:420] comment: This modification occurs naturally in two forms. At an interior peptide location it exists as aminoethanethionic acid (or aminoethanethioic O-acid). At the carboxyl-terminal it exists as aminoethanethiolic acid (or aminoethanethioic S-acid). subset: PSI-MOD_slim synonym: "1-thioglycine" EXACT UniProt-feature [] synonym: "2-amino-1-sulfanylethanone" EXACT RESID-alternate [] synonym: "aminoethanethioic acid" EXACT RESID-systematic [] synonym: "aminoethanethioic O-acid" EXACT RESID-alternate [] synonym: "aminoethanethioic S-acid" EXACT RESID-alternate [] synonym: "aminoethanethiolic acid" EXACT RESID-alternate [] synonym: "aminoethanethionic acid" EXACT RESID-alternate [] synonym: "aminothioacetic acid" EXACT RESID-alternate [] synonym: "Carboxy->Thiocarboxy" RELATED PSI-MS-label [] synonym: "S(O)Gly" EXACT PSI-MOD-short [] synonym: "thiocarboxylic acid" RELATED UniMod-description [] xref: DiffAvg: "16.07" xref: DiffFormula: "C 0 H 0 N 0 O -1 S 1" xref: DiffMono: "15.977156" xref: Formula: "C 2 H 3 N 1 S 1" xref: MassAvg: "73.12" xref: MassMono: "72.998620" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00749 ! sulfur substitution for oxygen is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00271 name: heme P460-bis-L-cysteine-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between two cysteine residues, the C-3' of a tyrosine residue, and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:8325841, PubMed:9095195, RESID:AA0266] comment: Cross-link 3. subset: PSI-MOD_slim synonym: "[7,12-bis((S)-1-[((R)-2-amino-2-carboxy)ethylsulfanyl]ethyl)-10-(2-hydroxy-5-[(S)-2-amino-2-carboxy]ethylphenyl)-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "biscysteinyl-tyrosinyl-heme" EXACT RESID-alternate [] synonym: "Heme (covalent; via 3 links)" EXACT UniProt-feature [] xref: DiffAvg: "614.47" xref: DiffFormula: "C 34 Fe 1 H 30 N 4 O 4 S 0" xref: DiffMono: "614.161643" xref: Formula: "C 49 Fe 1 H 49 N 7 O 8 S 2" xref: MassAvg: "983.93" xref: MassMono: "983.243341" xref: Origin: "C, C, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00272 name: O-(phospho-5'-adenosine)-L-threonine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-threonine residue and 5'-phosphoadenosine through a phosphodiester bond to form O-(phospho-5'-adenosine)-L-threonine." [PubMed:2989287, PubMed:8917428, RESID:AA0267, UniMod:405] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-(5'-adenosine phosphonoxy)butanoic acid" EXACT RESID-systematic [] synonym: "5'-adenylic-O3-L-threonine" EXACT RESID-alternate [] synonym: "AMP binding site" RELATED UniMod-description [] synonym: "beta-5'-adenylic-L-threonine" EXACT RESID-alternate [] synonym: "L-threonine monoanhydride with 5'-adenylic acid" EXACT RESID-alternate [] synonym: "O(gamma)-5'-adenylic-L-threonine" EXACT RESID-alternate [] synonym: "O3-(phospho-5'-adenosine)-L-threonine" EXACT RESID-alternate [] synonym: "O3-L-threonine 5'-adenosine phosphodiester" EXACT RESID-alternate [] synonym: "Phosphoadenosine" RELATED PSI-MS-label [] xref: DiffAvg: "329.21" xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1" xref: DiffMono: "329.052520" xref: Formula: "C 14 H 19 N 6 O 8 P 1" xref: MassAvg: "430.31" xref: MassMono: "430.100198" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01165 ! adenylated residue [Term] id: MOD:00273 name: tris-L-cysteinyl L-cysteine persulfido bis-L-glutamato L-histidino tetrairon disulfide trioxide namespace: PSI-MOD def: "modification from RESID" [PubMed:12764602, RESID:AA0268] comment: Cross-link 7; secondary to RESID:AA0269. subset: PSI-MOD_slim synonym: "4Fe-2S-3O cluster" EXACT RESID-alternate [] synonym: "hybrid four iron cluster 2" EXACT RESID-alternate [] synonym: "mu-1:2kappaO-oxido-mu-1:3kappaO-oxido-mu-2:4kappaO-oxido-mu-3:4kappaS-sulfido-mu3-2:3:4kappaS-sulfido-S-cysteinyl-N1'-histidino-O5-glutamato 1-iron-S5-cysteine persulfido-O5-glutamato 2-iron-3,4-bis-(S-cysteinyl iron)" EXACT RESID-systematic [] synonym: "prismane iron-sulfur cofactor [misnomer]" RELATED RESID-misnomer [] xref: DiffAvg: "360.52" xref: DiffFormula: "C 0 Fe 4 H -7 N 0 O 3 S 3" xref: DiffMono: "360.585932" xref: Formula: "C 28 Fe 4 H 34 N 9 O 14 S 7" xref: MassAvg: "1168.46" xref: MassMono: "1167.766769" xref: Origin: "C, C, C, C, E, E, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00274 name: L-cysteine persulfide namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to L-cysteine persulfide." [ChEBI:28839, PubMed:15096637, PubMed:4276457, PubMed:8161529, RESID:AA0269, UniMod:421] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-disulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-disulfanylpropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-hydrodisulfidopropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-hydropersulfidopropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-persulfhydrylpropanoic acid" EXACT RESID-alternate [] synonym: "3-(thiosulfeno)-alanine" EXACT RESID-alternate [] synonym: "Cysteine persulfide" EXACT UniProt-feature [] synonym: "persulfide" RELATED UniMod-description [] synonym: "S-sulfanylcysteine" EXACT RESID-alternate [] synonym: "Sulfide" RELATED PSI-MS-label [] synonym: "thiocysteine" EXACT RESID-alternate [] xref: DiffAvg: "32.06" xref: DiffFormula: "C 0 H 0 N 0 O 0 S 1" xref: DiffMono: "31.972071" xref: Formula: "C 3 H 5 N 1 O 1 S 2" xref: MassAvg: "135.21" xref: MassMono: "134.981256" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00275 name: 3'-(1'-L-histidyl)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-histidine residue and an L-tyrosine residue by a carbon-nitrogen bond to form 3'-(1'-L-histidyl)-L-tyrosine." [ChEBI:19837, PubMed:10338009, RESID:AA0270] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S)-2-amino-3-[1-(1-((S)-2-amino-2-carboxyethyl)-4-hydoxyphen-3-yl)imidazol-4-yl]propanoic acid" EXACT RESID-systematic [] synonym: "1'-histidyl-3'-tyrosine (His-Tyr)" EXACT UniProt-feature [] synonym: "3'-(N(epsilon)-histidyl)tyrosine" EXACT RESID-alternate [] synonym: "3'-(N1'-histidyl)tyrosine" EXACT RESID-alternate [] synonym: "3'-(pi-histidyl)tyrosine" EXACT RESID-alternate [] synonym: "3'-(pros-histidyl)tyrosine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" xref: Formula: "C 15 H 14 N 4 O 3" xref: MassAvg: "298.30" xref: MassMono: "298.106590" xref: Origin: "H, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00276 name: heme P460-bis-L-cysteine-L-lysine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between two cysteine residues, a lysine residue, and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:12709052, PubMed:9237682, RESID:AA0271] comment: Cross-link 3. subset: PSI-MOD_slim synonym: "bis-S-cysteinyl-N6-lysino-heme" EXACT RESID-alternate [] synonym: "Heme (covalent; via 3 links)" EXACT UniProt-feature [] xref: DiffAvg: "614.47" xref: DiffFormula: "C 34 Fe 1 H 30 N 4 O 4 S 0" xref: DiffMono: "614.161643" xref: Formula: "C 46 Fe 1 H 52 N 8 O 7 S 2" xref: MassAvg: "948.93" xref: MassMono: "948.274976" xref: Origin: "C, C, K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00277 name: 5-methyl-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to 5-methyl-L-arginine." [PubMed:10660523, PubMed:11875433, PubMed:9367957, RESID:AA0272, UniMod:34] subset: PSI-MOD_slim synonym: "(2S,5S)-2-amino-5-carbamimidamidohexanoic acid" EXACT RESID-systematic [] synonym: "2-amino-5-guanidinohexanoic acid" EXACT RESID-alternate [] synonym: "4-methylarginine [misnomer]" RELATED RESID-misnomer [] synonym: "5-methylarginine" EXACT UniProt-feature [] synonym: "5-methylated L-arginine" EXACT PSI-MOD-alternate [] synonym: "C5MeArg" EXACT PSI-MOD-short [] synonym: "delta-methylarginine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 14 N 4 O 1" xref: MassAvg: "170.21" xref: MassMono: "170.116761" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00414 ! monomethylated L-arginine is_a: MOD:00656 ! C-methylated residue [Term] id: MOD:00278 name: 2-methyl-L-glutamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamine residue to 2-methyl-L-glutamine." [PubMed:10660523, PubMed:11875433, PubMed:9367957, RESID:AA0273, UniMod:34] subset: PSI-MOD_slim synonym: "(S)-2-amino-2-methylpentanediamic acid" EXACT RESID-systematic [] synonym: "2-methylated L-glutamine" EXACT PSI-MOD-alternate [] synonym: "2-methylglutamine" EXACT UniProt-feature [] synonym: "2-methylglutamine" EXACT RESID-alternate [] synonym: "alpha-methylglutamine" EXACT RESID-alternate [] synonym: "C2MeGln" EXACT PSI-MOD-short [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 6 H 10 N 2 O 2" xref: MassAvg: "142.16" xref: MassMono: "142.074228" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00656 ! C-methylated residue is_a: MOD:00722 ! monomethylated L-glutamine [Term] id: MOD:00279 name: N-pyruvic acid 2-iminyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an Lcysteline residue to N-pyruvic acid 2-iminyl-L-cysteine." [PubMed:1388164, RESID:AA0274, UniMod:422] subset: PSI-MOD_slim synonym: "(R)-2-(1-carboxy-2-sulfanylethanimino)propanoic acid" EXACT RESID-systematic [] synonym: "N-pyruvate 2-iminyl-cysteine" EXACT UniProt-feature [] synonym: "N-pyruvic acid 2-iminyl" RELATED UniMod-description [] synonym: "PyruvicAcidIminyl" RELATED PSI-MS-label [] xref: DiffAvg: "70.05" xref: DiffFormula: "C 3 H 2 N 0 O 2 S 0" xref: DiffMono: "70.005479" xref: Formula: "C 6 H 8 N 1 O 3 S 1" xref: MassAvg: "174.20" xref: MassMono: "174.022489" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01170 ! pyruvic acid iminylated residue [Term] id: MOD:00280 name: N-pyruvic acid 2-iminyl-L-valine namespace: PSI-MOD def: "A protein modification that effectively converts an L-valine residue to N-pyruvic acid 2-iminyl-L-valine." [PubMed:2071591, RESID:AA0275, UniMod:422] subset: PSI-MOD_slim synonym: "(S)-2-(1-carboxy-2-methylpropanimino)propanoic acid" EXACT RESID-systematic [] synonym: "N-pyruvate 2-iminyl-valine" EXACT UniProt-feature [] synonym: "N-pyruvic acid 2-iminyl" RELATED UniMod-description [] synonym: "PyruvicAcidIminyl" RELATED PSI-MS-label [] xref: DiffAvg: "70.05" xref: DiffFormula: "C 3 H 2 N 0 O 2" xref: DiffMono: "70.005479" xref: Formula: "C 8 H 12 N 1 O 3" xref: MassAvg: "170.19" xref: MassMono: "170.081718" xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00920 ! modified L-valine residue is_a: MOD:01170 ! pyruvic acid iminylated residue [Term] id: MOD:00281 name: 3'-heme-L-histidine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between the pros nitrogen of a histidine residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:12119398, PubMed:12429096, PubMed:12486054, PubMed:9712585, RESID:AA0276] subset: PSI-MOD_slim synonym: "2-[1-(N3'-histidyl)ethyl]protoporphyrin IX" EXACT RESID-alternate [] synonym: "[7-ethenyl-12-((S)-1-[((R)-2-amino-2-carboxyethyl)-3H-imidazol-3-yl]ethyl)-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "Heme (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "N(delta)-histidyl heme" EXACT RESID-alternate [] synonym: "N3'-histidyl heme" EXACT RESID-alternate [] synonym: "pi-histidyl heme" EXACT RESID-alternate [] synonym: "pros-histidyl heme" EXACT RESID-alternate [] xref: DiffAvg: "616.49" xref: DiffFormula: "C 34 Fe 1 H 32 N 4 O 4" xref: DiffMono: "616.177293" xref: Formula: "C 40 Fe 1 H 39 N 7 O 5" xref: MassAvg: "753.63" xref: MassMono: "753.236205" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00282 name: S-selenyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-selenyl-L-cysteine." [PubMed:10430865, PubMed:10966817, PubMed:11827487, PubMed:12716131, PubMed:14594807, RESID:AA0277, UniMod:423] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(selanylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-hydroselenosulfidopropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-hydroselenylsulfidopropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-hydroselenylthiopropanoic acid" EXACT RESID-alternate [] synonym: "cysteine perselenide [misnomer]" RELATED RESID-misnomer [] synonym: "Delta:Se(1)" RELATED PSI-MS-label [] synonym: "S-selanylcysteine" EXACT UniProt-feature [] synonym: "S-selanylcysteine" EXACT RESID-alternate [] synonym: "S-selenylcysteine" EXACT RESID-alternate [] synonym: "selenyl" RELATED UniMod-description [] xref: DiffAvg: "78.96" xref: DiffFormula: "C 0 H 0 N 0 O 0 S 0 Se 1" xref: DiffMono: "79.916521" xref: Formula: "C 3 H 5 N 1 O 1 S 1 Se 1" xref: MassAvg: "182.10" xref: MassMono: "182.925706" xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00745 ! selenium containing residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00283 name: N6-propylamino-poly(propylmethylamino)-propyldimethylamine-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to an N6-propylamino-poly(propylmethylamino)-propyldimethylamine-L-lysine." [PubMed:10550045, PubMed:11349130, RESID:AA0278] subset: PSI-MOD_slim synonym: "(S)-2-amino-N6-(dimethylaminoprop-3-yl-poly[N-(methyl)aminoprop-3-yl]aminoprop-3-yl)aminohexanoic acid" EXACT RESID-systematic [] synonym: "lysine derivative Lys(x)" EXACT RESID-alternate [] synonym: "N6-[3-(N(omega)-dimethylaminopropyl-poly[3-(methylamino)propyl]amino)propyl]lysine" EXACT RESID-alternate [] synonym: "N6-poly(methylaminopropyl)lysine" EXACT UniProt-feature [] synonym: "silaffin polycationic lysine derivative" EXACT RESID-alternate [] xref: DiffAvg: "426.73" xref: DiffFormula: "C 24 H 54 N 6 O 0" xref: DiffMono: "426.440996" xref: Formula: "C 30 H 66 N 8 O 1" xref: MassAvg: "554.90" xref: MassMono: "554.535959" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00284 name: dihydroxyheme-L-aspartate ester-L-glutamate ester namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between an aspartic acid residue, a glutamic acid residue, and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:10447690, RESID:AA0279] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "1,5-bishydroxymethyl protoporphyrin IX 1-glutamate ester 5-aspartate ester" EXACT RESID-alternate [] synonym: "[13-[(S)-(4-amino-4-carboxy)butanoyloxymethyl]-3-[(S)-(3-amino-3-carboxy)propanoyloxymethyl]-7,12-diethenyl-8,17-dimethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "Heme (covalent; via 2 links)" EXACT UniProt-feature [] synonym: "peroxidase heme cofactor" EXACT RESID-alternate [] xref: DiffAvg: "612.46" xref: DiffFormula: "C 34 Fe 1 H 28 N 4 O 4" xref: DiffMono: "612.145993" xref: Formula: "C 43 Fe 1 H 40 N 6 O 10" xref: MassAvg: "856.66" xref: MassMono: "856.215529" xref: Origin: "D, E" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00285 name: dihydroxyheme-L-aspartate ester-L-glutamate ester-L-methionine sulfonium namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between an aspartic acid residue, a glutamic acid residue, a methionine residue (forming a sulfonium ether), and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:10447690, PubMed:10480885, PubMed:1320128, PubMed:7840679, RESID:AA0280] comment: Cross-link 3. subset: PSI-MOD_slim synonym: "1,5-bishydroxymethyl protoporphyrin IX 1-glutamate ester 5-aspartate ester 2-methionine sulfonium" EXACT RESID-alternate [] synonym: "[13-[(S)-(4-amino-4-carboxy)butanoyloxymethyl]-3-[(S)-(3-amino-3-carboxy)propanoyloxymethyl]-12-[(S)-(3-amino-3-carboxy)propylsulfoniumethyl]-7-ethenyl-8,17-dimethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "Heme (covalent; via 3 links)" EXACT UniProt-feature [] synonym: "myeloperoxidase heme cofactor" EXACT RESID-alternate [] xref: DiffAvg: "613.46" xref: DiffFormula: "C 34 Fe 1 H 29 N 4 O 4 S 0" xref: DiffMono: "613.153818" xref: Formula: "C 48 Fe 1 H 50 N 7 O 11 S 1" xref: MassAvg: "988.86" xref: MassMono: "988.263839" xref: Origin: "D, E, M" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00286 name: L-cysteinyl molybdenum bis(molybdopterin guanine dinucleotide) namespace: PSI-MOD def: "modification from RESID" [RESID:AA0281, UniMod:424] subset: PSI-MOD_slim synonym: "2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotide" EXACT RESID-alternate [] synonym: "bis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-cysteinyl-S-molybdenum" EXACT RESID-systematic [] synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED UniMod-description [] synonym: "MolybdopterinGD" RELATED PSI-MS-label [] xref: DiffAvg: "1572.03" xref: DiffFormula: "C 40 H 47 Mo 1 N 20 O 26 P 4 S 4" xref: DiffMono: "1572.985775" xref: Formula: "C 43 H 52 Mo 1 N 21 O 27 P 4 S 5" xref: MassAvg: "1675.18" xref: MassMono: "1675.994960" xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01167 ! molybdopterin guanine dinucleotide [Term] id: MOD:00287 name: (2S,3R,4S)-3,4-dihydroxyproline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to a (2S,3R,4S)-3,4-dihydroxyproline." [DeltaMass:0, PubMed:12686488, RESID:AA0282, UniMod:425] comment: From DeltaMass: Average Mass: 32. subset: PSI-MOD_slim synonym: "(2S,3R,4S)-3,4-dihydroxypyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] synonym: "(3R,4S)-3,4-dihydroxyproline" EXACT UniProt-feature [] synonym: "2-alpha-3-beta-4-beta-3,4-dihydroxyproline" EXACT RESID-alternate [] synonym: "3,4-dihydroxylated L-proline" EXACT PSI-MOD-alternate [] synonym: "3,4-Dihydroxylation (of Proline)" EXACT DeltaMass-label [] synonym: "34Hy2Pro" EXACT PSI-MOD-short [] synonym: "dihydroxy" RELATED UniMod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "trans-2,3-cis-3,4-dihydroxy-L-proline" EXACT RESID-alternate [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2" xref: DiffMono: "31.989829" xref: Formula: "C 5 H 7 N 1 O 3" xref: MassAvg: "129.11" xref: MassMono: "129.042593" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00866 ! dihydroxylated proline [Term] id: MOD:00288 name: pyrroloquinoline quinone namespace: PSI-MOD def: "modification from RESID" [ChEBI:18315, PubMed:1310505, PubMed:7665488, RESID:AA0283] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "2,4,6-tricarboxylic-pyrrolo[2,3-5,6]quinoline 8,9-quinone" EXACT RESID-alternate [] synonym: "2,7,9-tricarboxy-1H-pyrrolo(2,3-f)quinoline-4,5-dione" EXACT RESID-alternate [] synonym: "4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-5,6]quinoline-2,7,9-tricarboxylic acid" EXACT RESID-systematic [] synonym: "coenzyme PQQ" EXACT RESID-alternate [] synonym: "methoxatin" EXACT RESID-alternate [] synonym: "Pyrroloquinoline quinone (Glu-Tyr)" EXACT UniProt-feature [] xref: DiffAvg: "37.92" xref: DiffFormula: "C 0 H -10 N 0 O 3" xref: DiffMono: "37.906494" xref: Formula: "C 14 H 6 N 2 O 8" xref: MassAvg: "330.21" xref: MassMono: "330.012415" xref: Origin: "E, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00289 name: tris-L-cysteinyl L-N1'-histidino tetrairon tetrasulfide namespace: PSI-MOD def: "A protein modification that effectively converts three L-cysteine residues and an L-histidine residue to tris-L-cysteinyl L-N1'-histidino tetrairon tetrasulfide." [PubMed:9836629, RESID:AA0284] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "tetra-mu3-sulfidotris(S-cysteinyliron)(N1'-histidinoiron)" EXACT RESID-systematic [] xref: DiffAvg: "347.61" xref: DiffFormula: "C 0 Fe 4 H -4 N 0 O 0 S 4" xref: DiffMono: "347.596734" xref: Formula: "C 15 Fe 4 H 18 N 6 O 4 S 7" xref: MassAvg: "794.18" xref: MassMono: "793.683200" xref: Origin: "C, C, C, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00290 name: tris-L-cysteinyl L-N3'-histidino tetrairon tetrasulfide namespace: PSI-MOD def: "A protein modification that effectively converts three L-cysteine residues and an L-histidine residue to tris-L-cysteinyl L-N3'-histidino tetrairon tetrasulfide." [PubMed:7854413, RESID:AA0285] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "tetra-mu3-sulfidotris(S-cysteinyliron)(N3'-histidinoiron)" EXACT RESID-systematic [] xref: DiffAvg: "347.61" xref: DiffFormula: "C 0 Fe 4 H -4 N 0 O 0 S 4" xref: DiffMono: "347.596734" xref: Formula: "C 15 Fe 4 H 18 N 6 O 4 S 7" xref: MassAvg: "794.18" xref: MassMono: "793.683200" xref: Origin: "C, C, C, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00291 name: tris-L-cysteinyl L-aspartato tetrairon tetrasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:7819255, PubMed:9283079, RESID:AA0286] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "tetra-mu3-sulfidotris(S-cysteinyliron)(O4-aspartatoiron)" EXACT RESID-systematic [] xref: DiffAvg: "347.61" xref: DiffFormula: "C 0 Fe 4 H -4 N 0 O 0 S 4" xref: DiffMono: "347.596734" xref: Formula: "C 13 Fe 4 H 16 N 4 O 6 S 7" xref: MassAvg: "772.12" xref: MassMono: "771.651231" xref: Origin: "C, C, C, D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00292 name: N6-pyruvic acid 2-iminyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to N6-pyruvic acid 2-iminyl-L-lysine." [PubMed:1463470, PubMed:7853400, PubMed:9047371, RESID:AA0287, UniMod:422] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-(1-carboxy-ethylimino)hexanoic acid" EXACT RESID-systematic [] synonym: "N-pyruvic acid 2-iminyl" RELATED UniMod-description [] synonym: "PyruvicAcidIminyl" RELATED PSI-MS-label [] xref: DiffAvg: "70.05" xref: DiffFormula: "C 3 H 2 N 0 O 2" xref: DiffMono: "70.005479" xref: Formula: "C 9 H 14 N 2 O 3" xref: MassAvg: "198.22" xref: MassMono: "198.100442" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01170 ! pyruvic acid iminylated residue [Term] id: MOD:00293 name: tris-L-cysteinyl L-serinyl tetrairon tetrasulfide namespace: PSI-MOD def: "modification from RESID" [RESID:AA0288] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "tetra-mu3-sulfidotris(S-cysteinyliron)(O3-serinyliron)" EXACT RESID-systematic [] xref: DiffAvg: "347.61" xref: DiffFormula: "C 0 Fe 4 H -4 N 0 O 0 S 4" xref: DiffMono: "347.596734" xref: Formula: "C 12 Fe 4 H 16 N 4 O 5 S 7" xref: MassAvg: "744.11" xref: MassMono: "743.656317" xref: Origin: "C, C, C, S" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00294 name: bis-L-cysteinyl L-N3'-histidino L-serinyl tetrairon tetrasulfide namespace: PSI-MOD def: "modification from RESID" [RESID:AA0289] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "tetra-mu3-sulfidobis(S-cysteinyliron)(N3'-histidinoiron)(O3-serinyliron)" EXACT RESID-systematic [] xref: DiffAvg: "347.61" xref: DiffFormula: "C 0 Fe 4 H -4 N 0 O 0 S 4" xref: DiffMono: "347.596734" xref: Formula: "C 15 Fe 4 H 18 N 6 O 5 S 6" xref: MassAvg: "778.11" xref: MassMono: "777.706044" xref: Origin: "C, C, H, S" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00295 name: O-octanoyl-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-octanoyl-L-serine." [PubMed:10604470, PubMed:12716131, RESID:AA0290, UniMod:426] subset: PSI-MOD_slim synonym: "(2S)-2-amino-3-(octanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "L-serine octanoate ester" EXACT RESID-alternate [] synonym: "O-octanoyl serine" EXACT UniProt-feature [] synonym: "O-octanoylated L-serine" EXACT PSI-MOD-alternate [] synonym: "O3-octanoyl-L-serine" EXACT RESID-alternate [] synonym: "Octanoyl" RELATED PSI-MS-label [] synonym: "octanoyl" RELATED UniMod-description [] synonym: "OOctSer" EXACT PSI-MOD-short [] xref: DiffAvg: "126.20" xref: DiffFormula: "C 8 H 14 N 0 O 1" xref: DiffMono: "126.104465" xref: Formula: "C 11 H 19 N 1 O 3" xref: MassAvg: "213.27" xref: MassMono: "213.136493" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00669 ! O-octanoylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00296 name: O-D-glucuronosyl-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:10858503, PubMed:12716131, PubMed:7398618, RESID:AA0291, UniMod:54] subset: PSI-MOD_slim synonym: "(2S)-2-amino-3-glucuronosylpropanoic acid" EXACT RESID-systematic [] synonym: "Glucuronyl" RELATED PSI-MS-label [] synonym: "N-glucuronylation" RELATED UniMod-description [] synonym: "O-linked (HexA)" EXACT UniProt-feature [] synonym: "O3-D-glucuronosyl-L-serine" EXACT RESID-alternate [] xref: DiffAvg: "176.12" xref: DiffFormula: "C 6 H 8 N 0 O 6" xref: DiffMono: "176.032088" xref: Formula: "C 9 H 13 N 1 O 8" xref: MassAvg: "263.20" xref: MassMono: "263.064116" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00447 ! N-glucuronylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00297 name: tris-L-cysteinyl L-cysteine persulfido bis-L-glutamato L-histidino nickel triiron disulfide trioxide namespace: PSI-MOD def: "modification from RESID" [RESID:AA0292] comment: Cross-link 7; secondary to RESID:AA0269. subset: PSI-MOD_slim synonym: "carbon monoxide dehydrogenase nickel-iron cofactor" EXACT RESID-alternate [] synonym: "hybrid nickel-triiron cluster" EXACT RESID-alternate [] synonym: "mu-1:2kappaO-oxido-mu-1:3kappaO-oxido-mu-2:4kappaO-oxido-mu-3:4kappaS-sulfido-mu3-2:3:4kappaS-sulfido-S-cysteinyl-N1'-histidino-O5-glutamato 1-iron-S5-cysteine persulfido-O5-glutamato 2-nickel-3,4-bis-(S-cysteinyl iron)" EXACT RESID-systematic [] synonym: "Ni-3Fe-2S-3O cluster" EXACT RESID-alternate [] xref: DiffAvg: "363.37" xref: DiffFormula: "C 0 Fe 3 H -7 N 0 Ni 1 O 3 S 3" xref: DiffMono: "362.586337" xref: Formula: "C 28 Fe 3 H 34 N 9 Ni 1 O 14 S 7" xref: MassAvg: "1171.30" xref: MassMono: "1169.767174" xref: Origin: "C, C, C, C, E, E, H" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00741 ! nickel containing modified residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00298 name: tris-L-cysteinyl L-cysteine persulfido L-glutamato L-histidino L-serinyl nickel triiron disulfide trioxide namespace: PSI-MOD def: "modification from RESID" [PubMed:2550436, RESID:AA0293] comment: Cross-link 7; secondary to RESID:AA0269. subset: PSI-MOD_slim synonym: "carbon monoxide dehydrogenase nickel-iron cofactor" EXACT RESID-alternate [] synonym: "hybrid nickel-triiron cluster" EXACT RESID-alternate [] synonym: "mu-1:2kappaO-oxido-mu-1:3kappaO-oxido-mu-2:4kappaO-oxido-mu-3:4kappaS-sulfido-mu3-2:3:4kappaS-sulfido-S-cysteinyl-N1'-histidino-O5-glutamato 1-iron-S5-cysteine persulfido-O3-serinyl 2-nickel-3,4-bis-(S-cysteinyl iron)" EXACT RESID-systematic [] synonym: "Ni-3Fe-2S-3O cluster" EXACT RESID-alternate [] xref: DiffAvg: "363.37" xref: DiffFormula: "C 0 Fe 3 H -7 N 0 Ni 1 O 3 S 3" xref: DiffMono: "362.586337" xref: Formula: "C 26 Fe 3 H 32 N 9 Ni 1 O 13 S 7" xref: MassAvg: "1129.27" xref: MassMono: "1127.756609" xref: Origin: "C, C, C, C, E, H, S" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00741 ! nickel containing modified residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00299 name: N6-(L-isoaspartyl)-L-lysine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-aspartic acid residue and an L-lysine residue by an isopeptide bond to form N6-(L-isoaspartyl)-L-lysine." [ChEBI:21862, DeltaMass:0, PubMed:11000116, PubMed:6503713, RESID:AA0294] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S,S)-2-amino-6-[(3-amino-3-carboxypropanoyl)amino]hexanoic acid" EXACT RESID-systematic [] synonym: "beta-(N6-lysyl)aspartyl acid" EXACT RESID-alternate [] synonym: "Isoaspartyl lysine isopeptide (Lys-Asn) (interchain with N-...)" EXACT UniProt-feature [] synonym: "isoaspartyl N6-lysine" EXACT RESID-alternate [] synonym: "N-(beta-Aspartyl)-Lysine (Crosslink)" EXACT DeltaMass-label [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" xref: DiffMono: "-17.026549" xref: Formula: "C 10 H 15 N 3 O 3" xref: MassAvg: "225.24" xref: MassMono: "225.111341" xref: Origin: "K, N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00688 ! isopeptide crosslinked residues is_a: MOD:00903 ! modified L-asparagine residue is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00946 ! crosslinked residues with loss of ammonia [Term] id: MOD:00300 name: L-glutamyl-5-poly(ADP-ribose) namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to an L-glutamyl-5-poly(ADP-ribose)." [DeltaMass:0, PubMed:11246023, PubMed:15842200, PubMed:8533153, RESID:AA0295, UniMod:213] comment: From DeltaMass: Average Mass: 541. subset: PSI-MOD_slim synonym: "(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid" EXACT RESID-systematic [] synonym: "ADP Ribose addition" RELATED UniMod-description [] synonym: "ADP-Ribosyl" RELATED PSI-MS-label [] synonym: "L-isoglutamyl-poly(ADP-ribose)" EXACT RESID-alternate [] synonym: "O-ADP-ribosylation (on Glutamate or C terminus)" EXACT DeltaMass-label [] synonym: "PolyADP-ribosyl glutamic acid" EXACT UniProt-feature [] xref: DiffAvg: "541.30" xref: DiffFormula: "C 15 H 21 N 5 O 13 P 2" xref: DiffMono: "541.061109" xref: Formula: "C 20 H 28 N 6 O 16 P 2" xref: MassAvg: "670.41" xref: MassMono: "670.103702" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00752 ! adenosine diphosphoribosyl (ADP-ribosyl) modified residue is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00301 name: O-(N-acetylglucosamine-1-phosphoryl)-L-serine namespace: PSI-MOD def: "modification from RESID" [DeltaMass:0, PubMed:6438439, PubMed:6993483, PubMed:8631906, RESID:AA0296, UniMod:428] comment: From DeltaMass: Average Mass: 266 subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(2-acetamido-2-deoxy-D-glucopyranose alpha1-phosphonoxy)propanoic acid" EXACT RESID-systematic [] synonym: "N-acetylglucosamine-1-phosphoryl" RELATED UniMod-description [] synonym: "O-beta(N-acetyl-glucosamine-alpha1-phosphate)serine" EXACT RESID-alternate [] synonym: "O-GlcNAc-1-phosphorylation (of Serine)" EXACT DeltaMass-label [] synonym: "O-linked (P-GlcNAc)" EXACT UniProt-feature [] synonym: "O3-(N-acetylglucosamine-1-phosphoryl)-L-serine" EXACT RESID-alternate [] synonym: "O3-L-serine 2-(acetylamino)-2-deoxy-D-glucopyranose 1-phosphodiester" EXACT RESID-alternate [] synonym: "PhosphoHexNAc" RELATED PSI-MS-label [] xref: DiffAvg: "283.17" xref: DiffFormula: "C 8 H 14 N 1 O 8 P 1" xref: DiffMono: "283.045703" xref: Formula: "C 11 H 19 N 2 O 10 P 1" xref: MassAvg: "370.25" xref: MassMono: "370.077731" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00302 name: O-(phosphoglycosyl-D-mannose-1-phosphoryl)-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:10037765, PubMed:15649890, RESID:AA0297, UniMod:429] subset: PSI-MOD_slim synonym: "O-(alpha-D-mannosyl-1-phosphoryl)-L-serine" EXACT RESID-alternate [] synonym: "O-[alpha-D-mannopyranosyloxy(hydroxy)phosphoryl]-L-serine" EXACT RESID-systematic [] synonym: "O-linked (P-Man)" EXACT UniProt-feature [] synonym: "O3-(D-mannose-1-phosphoryl)-L-serine" EXACT RESID-alternate [] synonym: "O3-L-serine alpha-D-mannopyranose 1-phosphodiester" EXACT RESID-alternate [] synonym: "phosphoglycosyl-D-mannose-1-phosphoryl" RELATED UniMod-description [] synonym: "PhosphoHex" RELATED PSI-MS-label [] xref: DiffAvg: "242.12" xref: DiffFormula: "C 6 H 11 N 0 O 8 P 1" xref: DiffMono: "242.019154" xref: Formula: "C 9 H 16 N 1 O 10 P 1" xref: MassAvg: "329.20" xref: MassMono: "329.051182" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00303 name: heptakis-L-histidino tetracopper mu4-sulfide hydroxide namespace: PSI-MOD def: "modification from RESID" [PubMed:11024061, PubMed:11041839, RESID:AA0298] comment: Cross-link 7. subset: PSI-MOD_slim synonym: "mu4-sulfido bis(bis-N1'-histidino copper)(N1'-histidino-N3'-histidino copper)(N3'-histidino hydroxide copper)" EXACT RESID-systematic [] synonym: "nitrous oxide reductase nosZ CuZ cluster" EXACT RESID-alternate [] synonym: "pentakis-L-N1'-histidino-bis-L-N3'-histidino tetracopper sulfide hydroxide" EXACT RESID-alternate [] xref: DiffAvg: "296.20" xref: DiffFormula: "C 0 Cu 4 H -6 N 0 O 1 S 1" xref: DiffMono: "293.638425" xref: Formula: "C 42 Cu 4 H 43 N 21 O 8 S 1" xref: MassAvg: "1256.18" xref: MassMono: "1253.050808" xref: Origin: "H, H, H, H, H, H, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00742 ! copper containing modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00304 name: L-leucine methyl ester namespace: PSI-MOD def: "A protein modification that effectively converts an L-leucine residue to L-leucine methyl ester." [PubMed:10191253, PubMed:11875433, PubMed:8206937, RESID:AA0299, UniMod:34] comment: incidental to RESID:AA0039 subset: PSI-MOD_slim synonym: "2-amino-4-methylpentanoic methyl ester" EXACT RESID-alternate [] synonym: "alpha-aminoisocaproic methyl ester" EXACT RESID-alternate [] synonym: "Leucine methyl ester" EXACT UniProt-feature [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "methyl (S)-2-amino-4-methylpentanoate" EXACT RESID-systematic [] synonym: "methyl esterified L-leucine" EXACT PSI-MOD-alternate [] synonym: "methyl L-leucinate" EXACT RESID-alternate [] synonym: "Methylation" RELATED UniMod-description [] synonym: "OMeLeu" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 14 N 1 O 2" xref: MassAvg: "144.19" xref: MassMono: "144.102454" xref: Origin: "L" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00393 ! O-methylated residue is_a: MOD:00599 ! monomethylated residue is_a: MOD:00662 ! methylated leucine [Term] id: MOD:00305 name: hexakis-L-cysteinyl L-serinyl octairon heptasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:10525412, PubMed:12215645, PubMed:9063865, RESID:AA0300] comment: Cross-link 7; incidental to RESID:AA0141. subset: PSI-MOD_slim synonym: "Cys6Ser-[8Fe7S]" EXACT PSI-MOD-short [] synonym: "nitrogenase P-cluster" EXACT RESID-alternate [] xref: DiffAvg: "663.15" xref: DiffFormula: "C 0 Fe 8 H -8 N 0 O 0 S 7" xref: DiffMono: "663.221397" xref: Formula: "C 21 Fe 8 H 27 N 7 O 8 S 13" xref: MassAvg: "1369.09" xref: MassMono: "1368.308534" xref: Origin: "C, C, C, C, C, C, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00307 name: L-aspartimide namespace: PSI-MOD def: "A protein modification that effectively cyclizes an L-asparagine residue to form a carboxyl-terminal L-aspartimide." [DeltaMass:18, PubMed:12771378, PubMed:2378679, PubMed:7662664, PubMed:7988548, PubMed:9309583, RESID:AA0302, UniMod:23] comment: From DeltaMass: Average Mass: -17 Average Mass Change:-17 References:Clarke, S., Lability of Aspargine and Aspartic Acid Residues in Protein and Peptides, in: Stability of Protein Pharmaceuticals : Chemical and Physical Paths of Protein Degradation, Part A (T.J. Ahern and M.C. Manning, eds.), 1992,Plenum Press, New York, pp.1-29Xie, M.; Vander Velde, D.; Morton, M.; Borchardt, R.T.; Schowen,R.L.: pH-Induced Change in the Rate-Determining Step for the Hydrolysis of the Asp/Asn-Derived Cyclic-Imide Intermediate in Protein Degradation. (1996) J. Am. Chem. Soc. 118: 8955-8956. subset: PSI-MOD_slim synonym: "(S)-3-amino-2,5-pyrrolidinedione" EXACT RESID-systematic [] synonym: "2-amino-butanimide" EXACT RESID-alternate [] synonym: "alpha-aminosuccinimide" EXACT RESID-alternate [] synonym: "Dehydrated" RELATED UniMod-interim [] synonym: "Dehydration" RELATED UniMod-description [] synonym: "Succinimide formation from asparagine" EXACT DeltaMass-label [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 4 H 5 N 2 O 2" xref: MassAvg: "113.09" xref: MassMono: "113.035102" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00601 ! cyclized residue is_a: MOD:00704 ! dehydrated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00308 name: L-glutamimide namespace: PSI-MOD def: "A protein modification that effectively cyclizes an L-glutamine residue to form a carboxyl-terminal L-glutamimide." [PubMed:12771378, PubMed:14593103, RESID:AA0303, UniMod:23] subset: PSI-MOD_slim synonym: "(S)-3-amino-2,6-piperidinedione" EXACT RESID-systematic [] synonym: "2-aminopentanimide" EXACT RESID-alternate [] synonym: "alpha-aminoglutarimide" EXACT RESID-alternate [] synonym: "Dehydrated" RELATED UniMod-interim [] synonym: "Dehydration" RELATED UniMod-description [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 5 H 7 N 2 O 2" xref: MassAvg: "127.12" xref: MassMono: "127.050752" xref: Origin: "Q" xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00601 ! cyclized residue is_a: MOD:00704 ! dehydrated residue is_a: MOD:00907 ! modified L-glutamine residue [Term] id: MOD:00309 name: L-beta-carboxyaspartic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to L-beta-carboxyaspartic acid." [PubMed:6390094, PubMed:7138832, PubMed:7457858, PubMed:8135347, RESID:AA0304, UniMod:299] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-carboxybutanedioic acid" EXACT RESID-systematic [] synonym: "2-amino-1,1,2-ethanetricarboxylic acid" EXACT RESID-alternate [] synonym: "3-carboxyaspartic acid" EXACT RESID-alternate [] synonym: "Carboxy" RELATED UniMod-interim [] synonym: "Carboxylation" RELATED UniMod-description [] xref: DiffAvg: "44.01" xref: DiffFormula: "C 1 H 0 N 0 O 2" xref: DiffMono: "43.989829" xref: Formula: "C 5 H 5 N 1 O 5" xref: MassAvg: "159.10" xref: MassMono: "159.016772" xref: Origin: "D" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01152 ! carboxylated residue [Term] id: MOD:00310 name: N5-methyl-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to N5-methyl-L-arginine." [PubMed:11875433, PubMed:9792625, PubMed:9873020, RESID:AA0305, UniMod:34] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-[(amino-iminomethyl)(methyl)amino]pentanoic acid" EXACT RESID-systematic [] synonym: "delta-N-methylarginine" EXACT RESID-alternate [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "N5-methylarginine" EXACT UniProt-feature [] synonym: "N5-methylated L-arginine" EXACT PSI-MOD-alternate [] synonym: "N5MeArg" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 14 N 4 O 1" xref: MassAvg: "170.21" xref: MassMono: "170.116761" xref: Origin: "R" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00414 ! monomethylated L-arginine is_a: MOD:00602 ! N-methylated residue [Term] id: MOD:00311 name: L-cysteine coenzyme A disulfide namespace: PSI-MOD def: "modification from RESID" [DeltaMass:0, PubMed:1734967, RESID:AA0306, UniMod:281] comment: DeltaMass gives no formula with mass as 454. subset: PSI-MOD_slim synonym: "(2R)-2-amino-3-(2-((3-(((2R)-2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)amino)-1-oxopropyl)amino)ethyl)dithio-propanoic acid 4'-ester with adenosine 5'-(trihydrogen diphosphate) 3'-(dihydrogen phosphate)" EXACT RESID-systematic [] synonym: "coenzyme A L-cysteine mixed disulfide" EXACT RESID-alternate [] synonym: "CoenzymeA" RELATED PSI-MS-label [] synonym: "Cysteine modified Coenzyme A" RELATED UniMod-description [] synonym: "SCoACys" EXACT PSI-MOD-short [] xref: DiffAvg: "765.52" xref: DiffFormula: "C 21 H 34 N 7 O 16 P 3 S 1" xref: DiffMono: "765.099559" xref: Formula: "C 24 H 39 N 8 O 17 P 3 S 2" xref: MassAvg: "868.66" xref: MassMono: "868.108744" xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00312 name: S-myristoyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-myristoyl-L-cysteine." [PubMed:10026218, PubMed:10080938, PubMed:8824274, RESID:AA0307, UniMod:45] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(tetradecanoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "Myristoyl" RELATED PSI-MS-label [] synonym: "Myristoylation" RELATED UniMod-description [] synonym: "S-myristoylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "SMyrCys" EXACT PSI-MOD-short [] synonym: "tetradecanoate cysteine thioester" EXACT RESID-alternate [] xref: DiffAvg: "210.36" xref: DiffFormula: "C 14 H 26 N 0 O 1 S 0" xref: DiffMono: "210.198365" xref: Formula: "C 17 H 31 N 1 O 2 S 1" xref: MassAvg: "313.50" xref: MassMono: "313.207550" xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00655 ! S-myristoylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00313 name: S-palmitoleyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-palmitoleyl-L-cysteine." [PubMed:8294460, RESID:AA0308, UniMod:431] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-((Z)-9-hexadecenoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "cis-9-hexadecenoate cysteine thioester" EXACT RESID-alternate [] synonym: "Palmitoleyl" RELATED PSI-MS-label [] synonym: "palmitoleyl" RELATED UniMod-description [] synonym: "S-palmitoleylated L-cysteine" EXACT PSI-MOD-alternate [] synonym: "SPamD1Cys" EXACT PSI-MOD-short [] xref: DiffAvg: "236.39" xref: DiffFormula: "C 16 H 28 N 0 O 1 S 0" xref: DiffMono: "236.214016" xref: Formula: "C 19 H 33 N 1 O 2 S 1" xref: MassAvg: "339.54" xref: MassMono: "339.223200" xref: Origin: "C" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00672 ! S-acylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00314 name: glycine cholesterol ester namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to glycine cholesterol ester." [PubMed:11111088, PubMed:8824192, RESID:AA0309, UniMod:432] comment: Incidental to RESID:AA0060. UniMod origin corrected. [JSG] subset: PSI-MOD_slim synonym: "Cholesterol" RELATED UniMod-label [] synonym: "cholesterol ester" RELATED UniMod-description [] synonym: "Cholesterol glycine ester" EXACT UniProt-feature [] xref: DiffAvg: "368.64" xref: DiffFormula: "C 27 H 44 N 0 O 0" xref: DiffMono: "368.344301" xref: Formula: "C 29 H 48 N 1 O 2" xref: MassAvg: "442.70" xref: MassMono: "442.368505" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00315 name: pentakis-L-cysteinyl L-histidino nickel tetrairon pentasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:11509720, PubMed:2550436, RESID:AA0310] comment: Cross-link 6. subset: PSI-MOD_slim synonym: "carbon monoxide dehydrogenase nickel-iron cofactor" EXACT RESID-alternate [] synonym: "mu-1:2kappaS-sulfido-mu3-1:3:5kappaS-sulfido-mu3-2:3:4kappaS-sulfido-mu3-2:4:5kappaS-sulfido-mu3-3:4:5kappaS-sulfido-N1'-histidino-S-cysteinyl-1-iron-S-cysteinyl-2-nickel-3,4,5-tris-(S-cysteinyl iron)" EXACT RESID-systematic [] synonym: "Ni-4Fe-5S cluster" EXACT RESID-alternate [] xref: DiffAvg: "436.35" xref: DiffFormula: "C 0 Fe 4 H -6 N 0 Ni 1 O 0 S 5" xref: DiffMono: "435.488498" xref: Formula: "C 21 Fe 4 H 26 N 8 Ni 1 O 6 S 10" xref: MassAvg: "1089.20" xref: MassMono: "1087.593333" xref: Origin: "C, C, C, C, C, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00741 ! nickel containing modified residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00316 name: N4,N4-dimethyl-L-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to N4,N4-dimethyl-L-asparagine." [PubMed:12964758, PubMed:14570711, PubMed:8783012, RESID:AA0311, UniMod:36] subset: PSI-MOD_slim synonym: "(S)-2-amino-N4,N4-dimethylbutanediamic acid" EXACT RESID-systematic [] synonym: "beta-dimethylasparagine [misnomer]" RELATED RESID-misnomer [] synonym: "di-Methylation" RELATED UniMod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "N(gamma),N(gamma)-dimethylasparagine" EXACT RESID-alternate [] synonym: "N4,N4-dimethylasparagine" EXACT UniProt-feature [] synonym: "N4,N4-dimethylated L-asparagine" EXACT PSI-MOD-alternate [] synonym: "N4Me2Asn" EXACT PSI-MOD-short [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4 N 0 O 0" xref: DiffMono: "28.031300" xref: Formula: "C 6 H 10 N 2 O 2" xref: MassAvg: "142.16" xref: MassMono: "142.074228" xref: Origin: "N" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00429 ! dimethylated residue is_a: MOD:00602 ! N-methylated residue is_a: MOD:00673 ! methylated asparagine [Term] id: MOD:00317 name: N6-3,4-didehydroretinylidene-L-lysine namespace: PSI-MOD def: "modification from RESID" [PubMed:10717661, PubMed:3257009, PubMed:4056688, RESID:AA0312, UniMod:433] subset: PSI-MOD_slim synonym: "(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid" EXACT RESID-systematic [] synonym: "3,4-didehydroretinylidene" RELATED UniMod-description [] synonym: "Didehydroretinylidene" RELATED PSI-MS-label [] synonym: "N6-3-dehydroretinal-L-lysine" EXACT RESID-alternate [] synonym: "N6-3-dehydroretinyl-lysine" EXACT RESID-alternate [] xref: DiffAvg: "264.40" xref: DiffFormula: "C 20 H 24 N 0 O 0" xref: DiffMono: "264.187801" xref: Formula: "C 26 H 36 N 2 O 1" xref: MassAvg: "392.58" xref: MassMono: "392.282764" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00318 name: 4'-(S-L-cysteinyl)-L-tryptophyl quinone namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-tryptophan residue by a thioether bond to form 4'-(S-L-cysteinyl)-L-tryptophyl quinone." [PubMed:11555656, PubMed:11717396, RESID:AA0313] comment: Cross-link 2; secondary to RESID:AA0148. subset: PSI-MOD_slim synonym: "(S)-3-(2-amino-2-carboxyethyl)-4-[(R)-2-amino-2-carboxyethyl]sulfanyl-6,7-indolinedione" EXACT RESID-systematic [] synonym: "4'-cysteinyl-tryptophylquinone (Cys-Trp)" EXACT UniProt-feature [] synonym: "4-(S-cysteinyl)tryptophan-6,7-dione" EXACT RESID-alternate [] synonym: "cysteine tryptophylquinone" EXACT RESID-alternate [] xref: DiffAvg: "27.97" xref: DiffFormula: "C 0 H -4 N 0 O 2 S 0" xref: DiffMono: "27.958529" xref: Formula: "C 14 H 11 N 3 O 4 S 1" xref: MassAvg: "317.32" xref: MassMono: "317.047027" xref: Origin: "C, W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00319 name: 3-(S-L-cysteinyl)-L-aspartic acid namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-aspartic acid residue by a thioether bond to form 2-(S-L-cysteinyl)-L-aspartic acid." [PubMed:11555656, PubMed:11717396, RESID:AA0314] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S,3S)-2-amino-3-[(R)-2-amino-2-carboxyethyl]sulfanylbutanedioic acid" EXACT RESID-systematic [] synonym: "(2S,3S,6R)-2,6-diamino-3-carboxy-4-thiaheptanedioic acid" EXACT RESID-alternate [] synonym: "3-carboxy-L-lanthionine" EXACT RESID-alternate [] synonym: "3-cysteinyl-aspartic acid (Cys-Asp)" EXACT UniProt-feature [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 7 H 8 N 2 O 4 S 1" xref: MassAvg: "216.21" xref: MassMono: "216.020478" xref: Origin: "C, D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00320 name: 4-(S-L-cysteinyl)-L-glutamic acid namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-glutamic acid residue by a thioether bond to form 4-(S-L-cysteinyl)-L-glutamic acid." [ChEBI:20293, PubMed:11555656, PubMed:11717396, RESID:AA0315] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S,3S,7R)-2,7-diamino-4-carboxy-5-thiaoctanedioic acid" EXACT RESID-alternate [] synonym: "(2S,4S)-2-amino-4-[(R)-2-amino-2-carboxyethyl]sulfanylpentanedioic acid" EXACT RESID-systematic [] synonym: "4-cysteinyl-glutamic acid (Cys-Glu)" EXACT UniProt-feature [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 8 H 10 N 2 O 4 S 1" xref: MassAvg: "230.24" xref: MassMono: "230.036128" xref: Origin: "C, E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00321 name: cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid L-aspartate ester namespace: PSI-MOD def: "modification from RESID" [PubMed:11435437, PubMed:7949339, RESID:AA0316, UniMod:434] subset: PSI-MOD_slim synonym: "(7Z,14Xi)-14-[(S)-3-amino-3-carboxy-propanoyl]oxy-10,13-dioxo-7-heptadecenoic acid" EXACT RESID-systematic [] synonym: "barley lipid transfer protein modification" EXACT RESID-alternate [] synonym: "CHDH" RELATED PSI-MS-label [] synonym: "Cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid aspartate ester" EXACT UniProt-feature [] synonym: "cis-14-hydroxy-10,13-dioxo-7-heptadecenoic ester" RELATED UniMod-description [] xref: DiffAvg: "294.39" xref: DiffFormula: "C 17 H 26 N 0 O 4" xref: DiffMono: "294.183109" xref: Formula: "C 21 H 31 N 1 O 7" xref: MassAvg: "409.47" xref: MassMono: "409.210052" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00322 name: 1'-methyl-L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to tele-methyl-L-histidine." [PubMed:10601317, PubMed:11474090, PubMed:11875433, PubMed:6692818, PubMed:8076, PubMed:8645219, RESID:AA0317, UniMod:34] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1-methyl-1H-imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "3-methylhistidine [misnomer]" RELATED RESID-misnomer [] synonym: "4-methyl-histidine [misnomer]" RELATED RESID-misnomer [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "N(epsilon)-methylhistidine" EXACT RESID-alternate [] synonym: "NteleMeHis" EXACT PSI-MOD-short [] synonym: "tau-methylhistidine" EXACT RESID-alternate [] synonym: "tele-methylated L-histidine" EXACT PSI-MOD-alternate [] synonym: "Tele-methylhistidine" EXACT UniProt-feature [] synonym: "tele-methylhistidine" EXACT RESID-alternate [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 9 N 3 O 1" xref: MassAvg: "151.17" xref: MassMono: "151.074562" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00724 ! N-methylated L-histidine [Term] id: MOD:00323 name: L-lysine methyl ester namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to L-lysine methyl ester." [PubMed:10973948, PubMed:11875433, RESID:AA0318, UniMod:34] subset: PSI-MOD_slim synonym: "2,6-diaminohexanoic methyl ester" EXACT RESID-alternate [] synonym: "alpha,epsilon-diaminocaproic methyl ester" EXACT RESID-alternate [] synonym: "Lysine methyl ester" EXACT UniProt-feature [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "methyl (S)-2,6-diaminohexanoate" EXACT RESID-systematic [] synonym: "methyl esterified L-lysine" EXACT PSI-MOD-alternate [] synonym: "methyl L-lysinate" EXACT RESID-alternate [] synonym: "Methylation" RELATED UniMod-description [] synonym: "OMeLys" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 15 N 2 O 2" xref: MassAvg: "159.21" xref: MassMono: "159.113353" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00393 ! O-methylated residue is_a: MOD:00599 ! monomethylated residue is_a: MOD:00663 ! methylated lysine [Term] id: MOD:00324 name: L-serinyl molybdenum bis(molybdopterin guanine dinucleotide) namespace: PSI-MOD def: "modification from RESID" [PubMed:8658132, PubMed:8658134, RESID:AA0319] subset: PSI-MOD_slim synonym: "2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotide" EXACT RESID-alternate [] synonym: "bis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-O3-serinyl-molybdenum oxide" EXACT RESID-systematic [] xref: DiffAvg: "1588.03" xref: DiffFormula: "C 40 H 47 Mo 1 N 20 O 27 P 4 S 4" xref: DiffMono: "1588.980690" xref: Formula: "C 43 H 52 Mo 1 N 21 O 29 P 4 S 4" xref: MassAvg: "1675.11" xref: MassMono: "1676.012718" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00744 ! molybdenum pterin containing modification is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00325 name: L-beta-methylthioasparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to L-beta-methylthioasparagine." [RESID:AA0320, UniMod:39] subset: PSI-MOD_slim synonym: "(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid" EXACT RESID-systematic [] synonym: "3-carboxamido-S-methyl-cysteine" EXACT RESID-alternate [] synonym: "3-methylthio-asparagine" EXACT RESID-alternate [] synonym: "beta-methylthio-asparagine" EXACT RESID-alternate [] synonym: "Beta-methylthiolation" RELATED UniMod-description [] synonym: "Methylthio" RELATED UniMod-interim [] xref: DiffAvg: "46.09" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 1" xref: DiffMono: "45.987721" xref: Formula: "C 5 H 8 N 2 O 2 S 1" xref: MassAvg: "160.19" xref: MassMono: "160.030649" xref: Origin: "N" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00903 ! modified L-asparagine residue is_a: MOD:01153 ! methylthiolated residue [Term] id: MOD:00326 name: L-pyrrolysine (Lys) namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to L-pyrrolysine (not known as a natural, post-translational modification process)." [PubMed:11435424, PubMed:12029131, PubMed:12029132, PubMed:15314242, PubMed:16096277, RESID:AA0321, UniMod:435] comment: This entry is for the artifactual formation of L-pyrrolysine from lysine. For encoded L-pyrrolysine, use PSI-MOD:01187. subset: PSI-MOD_slim synonym: "Pyl(Lys)" EXACT PSI-MOD-short [] synonym: "Pyrrolysine" EXACT UniProt-feature [] xref: DiffAvg: "109.13" xref: DiffFormula: "C 6 H 7 N 1 O 1" xref: DiffMono: "109.052764" xref: Formula: "C 12 H 19 N 3 O 2" xref: MassAvg: "237.30" xref: MassMono: "237.147727" xref: Origin: "K" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:01187 ! L-pyrrolysine residue [Term] id: MOD:00327 name: 3-hydroxy-L-tryptophan namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to a 3-hydroxy-L-tryptophan." [PubMed:10024453, PubMed:11457355, RESID:AA0322] subset: PSI-MOD_slim synonym: "(2S,3S)-2-amino-3-hydroxy-3-(1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "3-hydroxylated L-tryptophan" EXACT PSI-MOD-alternate [] synonym: "3-hydroxytryptophan" EXACT UniProt-feature [] synonym: "3-hydroxytryptophan" EXACT RESID-alternate [] synonym: "3HyTrp" EXACT PSI-MOD-short [] synonym: "beta-hydroxytryptophan" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 11 H 10 N 2 O 2" xref: MassAvg: "202.21" xref: MassMono: "202.074228" xref: Origin: "W" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00328 name: O4'-(phospho-3'-DNA)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-tyrosine residue and the 3'-end of DNA through a phosphodiester bond to form O4'-(phospho-3'-DNA)-L-tyrosine." [PubMed:2211714, RESID:AA0323] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[4-(3'-deoxyribonucleic acid phosphonoxy)phenyl]propanoic acid" EXACT RESID-systematic [] synonym: "O-(3'-phospho-DNA)-tyrosine" EXACT UniProt-feature [] synonym: "O4'-L-tyrosine 3'-DNA phosphodiester" EXACT RESID-alternate [] xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 9 H 10 N 1 O 5 P 1" xref: MassAvg: "243.15" xref: MassMono: "243.029659" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00750 ! deoxyribonucleic acid linked residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00329 name: hydroxyheme-L-glutamate ester namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between a glutamic acid residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:11139583, PubMed:11821421, PubMed:11980497, RESID:AA0324, UniMod:436] subset: PSI-MOD_slim synonym: "5-hydroxymethyl protoporphyrin IX 5-glutamate ester" EXACT RESID-alternate [] synonym: "[3-[(S)-(4-amino-4-carboxy)butanoyloxymethyl]-7,12-diethenyl-8,13,17-trimethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "cytochrome P450 CYP4A family heme cofactor" EXACT RESID-alternate [] synonym: "Heme (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "Hydroxyheme" RELATED PSI-MS-label [] synonym: "hydroxyheme" RELATED UniMod-description [] xref: DiffAvg: "614.47" xref: DiffFormula: "C 34 Fe 1 H 30 N 4 O 4" xref: DiffMono: "614.161643" xref: Formula: "C 39 Fe 1 H 37 N 5 O 7" xref: MassAvg: "743.59" xref: MassMono: "743.204236" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00330 name: (phospho-5'-guanosine)-L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to a (phospho-5'-guanosine)-L-histidine." [PubMed:10529169, PubMed:10869342, PubMed:7559521, RESID:AA0325, UniMod:413] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(5'-guanosine phosphono-imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "5'-guanylic-L-histidine" EXACT RESID-alternate [] synonym: "guanylylated histidine" EXACT RESID-alternate [] synonym: "L-histidine 5'-guanosine phosphoramidester" EXACT RESID-alternate [] synonym: "L-histidine monoanhydride with 5'-guanylic acid" EXACT RESID-alternate [] synonym: "phospho-guanosine" RELATED UniMod-description [] synonym: "Phosphoguanosine" RELATED PSI-MS-label [] xref: DiffAvg: "345.21" xref: DiffFormula: "C 10 H 12 N 5 O 7 P 1" xref: DiffMono: "345.047434" xref: Formula: "C 16 H 19 N 8 O 8 P 1" xref: MassAvg: "482.34" xref: MassMono: "482.106346" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01163 ! guanylated residue [Term] id: MOD:00331 name: tetrakis-L-cysteinyl triiron tetrasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:11592901, PubMed:11941493, PubMed:2511202, PubMed:6094558, RESID:AA0326] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "bis[bis-L-cysteinyl iron disulfido]iron" EXACT RESID-alternate [] synonym: "di-mu-1:2kappaS-sulfido di-mu-2:3kappaS-sulfido iron bis(bis-S-cysteinyliron)" EXACT RESID-systematic [] synonym: "tetra-mu-sulfido tetrakis-S-L-cysteinyl triiron" EXACT RESID-alternate [] synonym: "tetrakis-L-cysteinyl linear [3Fe-4S] cluster" EXACT RESID-alternate [] synonym: "tetrakis-L-cysteinyl triiron tetrasulfide D2 cluster" EXACT RESID-alternate [] xref: DiffAvg: "291.76" xref: DiffFormula: "C 0 Fe 3 H -4 N 0 O 0 S 4" xref: DiffMono: "291.661796" xref: Formula: "C 12 Fe 3 H 16 N 4 O 4 S 8" xref: MassAvg: "704.33" xref: MassMono: "703.698535" xref: Origin: "C, C, C, C" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00332 name: omega-N-glucosyl-L-arginine namespace: PSI-MOD def: "A protein modification that effectively forms an N4-glucosyl-arginine." [PubMed:15279557, PubMed:8521968, PubMed:9536051, RESID:AA0327, UniMod:41] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-[beta-glucopyranosyl(imino(methylamino)methyl)amino]pentanoic acid" EXACT RESID-systematic [] synonym: "Hex" RELATED PSI-MS-label [] synonym: "Hexose" RELATED UniMod-description [] synonym: "NG-beta-D-glucosylarginine" EXACT RESID-alternate [] synonym: "omega-N-(beta-D-glucosyl)-L-arginine" EXACT RESID-alternate [] synonym: "omega-N-glycosyl-L-arginine" EXACT RESID-alternate [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 12 H 22 N 4 O 6" xref: MassAvg: "318.33" xref: MassMono: "318.153934" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00006 ! N-glycosylated residue is_a: MOD:00433 ! glucosylated residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00333 name: (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to (3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5'-adenosine." [PubMed:7559516, PubMed:7835418, PubMed:8183363, RESID:AA0328, UniMod:437] comment: UniMod origin corrected. [JSG] subset: PSI-MOD_slim synonym: "(3-aminopropyl)(L-aspartyl-1-amino)phosphoryl-5-adenosine" RELATED UniMod-description [] synonym: "MicrocinC7" RELATED UniMod-label [] xref: DiffAvg: "386.30" xref: DiffFormula: "C 13 H 19 N 6 O 6 P 1" xref: DiffMono: "386.110369" xref: Formula: "C 17 H 26 N 8 O 9 P 1" xref: MassAvg: "517.41" xref: MassMono: "517.156036" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00701 ! nucleotide or nucleic acid modified residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00334 name: 1'-heme-L-histidine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between the tele nitrogen of a histidine residue and the porphyrin compound heme b, (7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-dipropanoato)iron." [PubMed:12033922, PubMed:12121092, RESID:AA0329, UniMod:390] subset: PSI-MOD_slim synonym: "(S)-[7-ethenyl-12-[1-((2-amino-2-carboxyethyl)-1H-imidazol-1-yl)ethyl]-3,8,13,17-tetramethyl-21H,23H-porphine-2,18-bis(2-carboxyethyl)-N21,N22,N23,N24]-ferrate" EXACT RESID-systematic [] synonym: "2-[1-(N1'-histidyl)ethyl]protoporphyrin IX" EXACT RESID-alternate [] synonym: "Heme" RELATED PSI-MS-label [] synonym: "heme" RELATED UniMod-description [] synonym: "Heme (covalent; via 1 link)" EXACT UniProt-feature [] synonym: "N(epsilon)-histidyl heme" EXACT RESID-alternate [] synonym: "N1'-histidyl heme" EXACT RESID-alternate [] synonym: "tau-histidyl heme" EXACT RESID-alternate [] synonym: "tele-histidyl heme" EXACT RESID-alternate [] xref: DiffAvg: "616.49" xref: DiffFormula: "C 34 Fe 1 H 32 N 4 O 4" xref: DiffMono: "616.177293" xref: Formula: "C 40 Fe 1 H 39 N 7 O 5" xref: MassAvg: "753.63" xref: MassMono: "753.236205" xref: Origin: "H" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00699 ! porphyrin modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00335 name: 3-methyl-L-lanthionine sulfoxide namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-threonine residue by a thioether bond to form 3-methyl-L-lanthionine sulfoxide." [PubMed:7737178, PubMed:9219543, RESID:AA0330] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S,3S,4Xi,6R)-2,6-diamino-3-methyl-4-oxo-4-thiaheptanedioic acid" EXACT RESID-alternate [] synonym: "(2S,3S,SXi)-2-amino-3-([(R)-2-amino-2-carboxyethyl]sulfinyl)butanoic acid" EXACT RESID-systematic [] synonym: "3-methyl-L-lanthionine S-oxide" EXACT RESID-alternate [] synonym: "Beta-methyllanthionine sulfoxide (Thr-Cys)" EXACT UniProt-feature [] synonym: "S-oxy-3-methyllanthionine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 7 H 10 N 2 O 3 S 1" xref: MassAvg: "202.23" xref: MassMono: "202.041213" xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00336 name: tris-L-cysteinyl L-aspartato diiron disulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:10968624, PubMed:1312028, PubMed:7947772, RESID:AA0331] comment: Cross-link 4 subset: PSI-MOD_slim synonym: "di-mu-sulfido(bis-S-cysteinyliron)(S-cysteinyl-O4-aspartatoiron)" EXACT RESID-systematic [] xref: DiffAvg: "171.79" xref: DiffFormula: "C 0 Fe 2 H -4 N 0 O 0 S 2" xref: DiffMono: "171.782717" xref: Formula: "C 13 Fe 2 H 16 N 4 O 6 S 5" xref: MassAvg: "596.30" xref: MassMono: "595.837214" xref: Origin: "C, C, C, D" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00337 name: S-carbamoyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-carbamoyl-L-cysteine." [PubMed:12586941, PubMed:240389, RESID:AA0332] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(carbamoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(aminocarbonyl)sulfanylpropanoic acid" EXACT RESID-alternate [] synonym: "2-amino-3-(aminocarbonyl)thiopropanoic acid" EXACT RESID-alternate [] synonym: "alpha-amino-beta-carbamylthiopropionic acid" EXACT RESID-alternate [] synonym: "beta-carbamylthioalanine" EXACT RESID-alternate [] synonym: "S-(aminocarbonyl)cysteine" EXACT RESID-alternate [] synonym: "S-carbamoylcysteine" EXACT RESID-alternate [] synonym: "S-carbamylcysteine" EXACT RESID-alternate [] synonym: "S-cysteinyl carbamate ester" EXACT RESID-alternate [] xref: DiffAvg: "43.02" xref: DiffFormula: "C 1 H 1 N 1 O 1 S 0" xref: DiffMono: "43.005814" xref: Formula: "C 4 H 6 N 2 O 2 S 1" xref: MassAvg: "146.17" xref: MassMono: "146.014998" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00398 ! carbamylated residue by cyanate or urea derivatization is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00338 name: S-cyano-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-cyano-L-cysteine." [PubMed:12586941, PubMed:4808702, RESID:AA0333, UniMod:438] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-thiocyanatopropanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-thiocyanatopropionic acid" EXACT RESID-alternate [] synonym: "beta-thiocyanatoalanine" EXACT RESID-alternate [] synonym: "Cyano" RELATED PSI-MS-label [] synonym: "cyano" RELATED UniMod-description [] synonym: "S-cyanocysteine" EXACT RESID-alternate [] synonym: "serine thiocyanic acid ester" EXACT RESID-alternate [] xref: DiffAvg: "25.01" xref: DiffFormula: "C 1 H -1 N 1 O 0 S 0" xref: DiffMono: "24.995249" xref: Formula: "C 4 H 4 N 2 O 1 S 1" xref: MassAvg: "128.15" xref: MassMono: "128.004434" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00339 name: L-cysteinyl hydrogenase diiron subcluster namespace: PSI-MOD def: "modification from RESID" [PubMed:10694885, PubMed:9836629, RESID:AA0334, UniMod:439] comment: incidental to RESID:AA0140 subset: PSI-MOD_slim synonym: "Diironsubcluster" RELATED PSI-MS-label [] synonym: "hydrogenase diiron subcluster" RELATED UniMod-description [] xref: DiffAvg: "342.88" xref: DiffFormula: "C 5 Fe 2 H -1 N 2 O 5 S 2" xref: DiffMono: "342.786913" xref: Formula: "C 8 Fe 2 H 4 N 3 O 6 S 3" xref: MassAvg: "446.02" xref: MassMono: "445.796098" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00738 ! iron containing modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00340 name: S-amidino-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-amidino-L-cysteine." [PubMed:9148748, RESID:AA0335, UniMod:440] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-amidinosulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-amidinothiopropanoic acid" EXACT RESID-alternate [] synonym: "alpha-amino-beta-thiocyanatopropionic acid" EXACT RESID-alternate [] synonym: "Amidino" RELATED PSI-MS-label [] synonym: "amidino" RELATED UniMod-description [] synonym: "beta-(S-isothiourea)alanine" EXACT RESID-alternate [] synonym: "beta-amidinothioalanine" EXACT RESID-alternate [] synonym: "S-amidinocysteine" EXACT RESID-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 1 H 2 N 2 O 0 S 0" xref: DiffMono: "42.021798" xref: Formula: "C 4 H 7 N 3 O 1 S 1" xref: MassAvg: "145.18" xref: MassMono: "145.030983" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00341 name: N-methyl-L-isoleucine namespace: PSI-MOD def: "A protein modification that effectively converts an L-isoleucine residue to N-methyl-L-isoleucine." [PubMed:11875433, RESID:AA0336, UniMod:34] subset: PSI-MOD_slim synonym: "(2S,3S)-2-methylamino-3-methylpentanoic acid" EXACT RESID-systematic [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "N-methylated L-isoleucine" EXACT PSI-MOD-alternate [] synonym: "N-methylisoleucine" EXACT UniProt-feature [] synonym: "N-methylisoleucine" EXACT RESID-alternate [] synonym: "NMeIle" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 13 N 1 O 1" xref: MassAvg: "127.18" xref: MassMono: "127.099714" xref: Origin: "I" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00715 ! methylated isoleucine [Term] id: MOD:00342 name: N-methyl-L-leucine namespace: PSI-MOD def: "A protein modification that effectively converts an L-leucine residue to N-methyl-L-leucine." [PubMed:11875433, RESID:AA0337, UniMod:34] subset: PSI-MOD_slim synonym: "(S)-2-methylamino-4-methylpentanoic acid" EXACT RESID-systematic [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] synonym: "N-methylated L-leucine" EXACT PSI-MOD-alternate [] synonym: "N-methylleucine" EXACT UniProt-feature [] synonym: "N-methylleucine" EXACT RESID-alternate [] synonym: "NMeLeu" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 13 N 1 O 1" xref: MassAvg: "127.18" xref: MassMono: "127.099714" xref: Origin: "L" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00662 ! methylated leucine [Term] id: MOD:00343 name: N-methyl-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to N-methyl-L-tyrosine." [DeltaMass:0, RESID:AA0338] subset: PSI-MOD_slim synonym: "(S)-2-methylamino-3-(4-hydoxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "N-methyl Tyrosinyl [misnomer]" EXACT DeltaMass-label [] synonym: "N-methylated L-tyrosine" EXACT PSI-MOD-alternate [] synonym: "N-methyltyrosine" EXACT UniProt-feature [] synonym: "N-methyltyrosine" EXACT RESID-alternate [] synonym: "NMeTyr" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 10 H 11 N 1 O 2" xref: MassAvg: "177.20" xref: MassMono: "177.078979" xref: Origin: "Y" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00718 ! methylated tyrosine [Term] id: MOD:00344 name: N-palmitoylglycine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-palmitoylglycine." [PubMed:12574119, RESID:AA0339, UniMod:47] comment: incidental to RESID:AA0060 subset: PSI-MOD_slim synonym: "N-palmitoyl glycine" EXACT UniProt-feature [] synonym: "N-palmitoylated glycine" EXACT PSI-MOD-alternate [] synonym: "NPamGly" EXACT PSI-MOD-short [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 N 0 O 1 S 0" xref: DiffMono: "238.229666" xref: Formula: "C 18 H 34 N 1 O 2" xref: MassAvg: "296.47" xref: MassMono: "296.258954" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00651 ! N-palmitoylated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00345 name: 2-(S-L-cysteinyl)-L-phenylalanine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-phenylalanine residue by a thioether bond to form 2-(S-L-cysteinyl)-L-phenylalanine." [PubMed:12696888, PubMed:3936839, RESID:AA0340] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2R,5R)-2,5-diamino-3-thia-2-phenylmethylhexanedioic acid" EXACT RESID-alternate [] synonym: "(R)-2-amino-2-[(R)-2-amino-2-carboxyethyl]sulfanyl-3-phenylethanoic acid" EXACT RESID-systematic [] synonym: "2-cysteinyl-L-phenylalanine (Cys-Phe)" EXACT UniProt-feature [] synonym: "alpha-(S-L-cysteinyl)-L-phenylalanine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 12 H 12 N 2 O 2 S 1" xref: MassAvg: "248.30" xref: MassMono: "248.061949" xref: Origin: "C, F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:00346 name: 2-(S-L-cysteinyl)-D-phenylalanine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-phenylalanine residue by a thioether bond to form 2-(S-L-cysteinyl)-D-phenylalanine." [PubMed:12696888, PubMed:3936839, RESID:AA0341] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S,5R)-2,5-diamino-3-thia-2-phenylmethylhexanedioic acid" EXACT RESID-alternate [] synonym: "(S)-2-amino-2-[(R)-2-amino-2-carboxyethyl]sulfanyl-3-phenylethanoic acid" EXACT RESID-systematic [] synonym: "2-cysteinyl-D-phenylalanine (Cys-Phe)" EXACT UniProt-feature [] synonym: "alpha-(S-L-cysteinyl)-D-phenylalanine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 12 H 12 N 2 O 2 S 1" xref: MassAvg: "248.30" xref: MassMono: "248.061949" xref: Origin: "C, F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:00347 name: 2-(S-L-cysteinyl)-D-allo-threonine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-threonine residue by a thioether bond to form 2-(S-L-cysteinyl)-D-allo-threonine." [PubMed:12696888, PubMed:3936839, RESID:AA0342] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2R,5S,6R)-2,5-diamino-5-carboxy-6-hydroxy-4-thiaheptanoic acid" EXACT RESID-alternate [] synonym: "(2S,3R)-2-amino-2-[(R)-2-amino-2-carboxyethyl]sulfanyl-3-hydroxybutanoic acid" EXACT RESID-systematic [] synonym: "2-cysteinyl-D-allo-threonine (Cys-Thr)" EXACT UniProt-feature [] synonym: "alpha-(S-L-cysteinyl)-D-allo-threonine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 7 H 10 N 2 O 3 S 1" xref: MassAvg: "202.23" xref: MassMono: "202.041213" xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00348 name: N-carbamoyl-L-alanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to N-carbamoyl-L-alanine." [PubMed:12203680, RESID:AA0343] subset: PSI-MOD_slim synonym: "(S)-2-(carbamoylamino)propanoic acid" EXACT RESID-systematic [] synonym: "2-ureidopropanoic acid" EXACT RESID-alternate [] synonym: "N-carbamylalanine" EXACT RESID-alternate [] xref: DiffAvg: "43.02" xref: DiffFormula: "C 1 H 1 N 1 O 1" xref: DiffMono: "43.005814" xref: Formula: "C 4 H 7 N 2 O 2" xref: MassAvg: "115.11" xref: MassMono: "115.050752" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00398 ! carbamylated residue by cyanate or urea derivatization is_a: MOD:00901 ! modified L-alanine residue [Term] id: MOD:00349 name: 4-amino-3-isothiazolidinone-L-serine namespace: PSI-MOD def: "modification from RESID" [PubMed:12802338, PubMed:12802339, RESID:AA0344] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(4R)-2-((S)-1-carboxy-2-hydroxyethyl)-4-amino-3(2H)-isothiazolidinone" EXACT RESID-systematic [] synonym: "2-(4-amino-3-oxo-isothiazolidin-2-yl)-3-hydroxy-propanoic acid" EXACT RESID-alternate [] synonym: "4-amino-3-isothiazolidinone serine (Cys-Ser)" EXACT UniProt-feature [] synonym: "cysteine sulfenyl amide cross-link" EXACT RESID-alternate [] synonym: "cysteine sulphenyl amide cross-link" EXACT RESID-alternate [] synonym: "N,N-(L-cystein-sulphen-1,S-diyl)-L-serine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 6 H 8 N 2 O 3 S 1" xref: MassAvg: "188.20" xref: MassMono: "188.025563" xref: Origin: "C, S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00350 name: L-threonyl-pentaglycyl-murein peptidoglycan namespace: PSI-MOD def: "modification from RESID" [PubMed:10754567, PubMed:1638631, RESID:AA0345] subset: PSI-MOD_slim synonym: "(2R,6S)-2-(N-mureinyl-(R)-alanyl-(S)-isoglutamyl)amino-6-(threonyl-pentaglycyl)amino-pimeloyl-(S)-alanyl-(S)-alanine" EXACT RESID-alternate [] synonym: "Pentaglycyl murein peptidoglycan amidated threonine" EXACT UniProt-feature [] xref: DiffAvg: "268.25" xref: DiffFormula: "C 10 H 14 N 5 O 4" xref: DiffMono: "268.104579" xref: Formula: "C 14 H 22 N 6 O 7" xref: MassAvg: "386.36" xref: MassMono: "386.154997" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01159 ! peptidoglycanated residue [Term] id: MOD:00351 name: N-glycyl-1-(phosphatidyl)ethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to N-glycyl-1-(phosphatidyl)ethanolamine." [PubMed:11100732, RESID:AA0346] subset: PSI-MOD_slim synonym: "(R)-1-hexadecanoyloxy-2-((Z)-9-octadecenoyloxy)-3-[2-(aminoacetylamino)ethyloxyphospho]propane" EXACT RESID-systematic [] synonym: "N-glycyl-1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine" EXACT RESID-alternate [] synonym: "Phosphatidylethanolamine amidated glycine" EXACT UniProt-feature [] xref: DiffAvg: "699.98" xref: DiffFormula: "C 39 H 74 N 1 O 7 P 1" xref: DiffMono: "699.520290" xref: Formula: "C 41 H 78 N 2 O 9 P 1" xref: MassAvg: "774.04" xref: MassMono: "773.544494" xref: Origin: "G" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00908 ! modified glycine residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00352 name: L-glutamyl 5-omega-hydroxyceramide ester namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to L-glutamyl 5-omega-hydroxyceramide ester." [PubMed:10411887, PubMed:9651377, RESID:AA0347] subset: PSI-MOD_slim synonym: "(S)-2-amino-5-[30-((2S,3R,4E)-1,3-dihydroxyicos-4-en-2-ylamino)-30-oxotriacontan-1-yloxy]-5-oxopentanoic acid" EXACT RESID-systematic [] synonym: "2-[30-(isoglutamyloxy)triacontanoyl]icosasphingosine" EXACT RESID-alternate [] synonym: "Omega-hydroxyceramide glutamate ester" EXACT UniProt-feature [] xref: DiffAvg: "761.29" xref: DiffFormula: "C 50 H 96 N 0 O 4" xref: DiffMono: "760.730862" xref: Formula: "C 55 H 104 N 2 O 6" xref: MassAvg: "889.42" xref: MassMono: "888.789439" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00907 ! modified L-glutamine residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00353 name: S-[5'-(L-tryptoph-6'-yl)-L-tyrosin-3'-yl]-L-methionin-S-ium namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue, an L-tyrosine residue, and an L-methionine residue to S-[5'-(L-tryptoph-6'-yl)-L-tyrosin-3'-yl]-L-methionin-S-ium." [PubMed:12172540, PubMed:16285713, RESID:AA0348] comment: Cross-link 3. subset: PSI-MOD_slim synonym: "Tryptophyl-tyrosyl-methioninium (Tyr-Met) (with W-...)" EXACT UniProt-feature [] xref: DiffAvg: "-3.02" xref: DiffFormula: "C 0 H -3 N 0 O 0 S 0" xref: DiffMono: "-3.023475" xref: FormalCharge: "1+" xref: Formula: "C 25 H 25 N 4 O 4 S 1" xref: MassAvg: "477.55" xref: MassMono: "477.159103" xref: Origin: "M, W, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00913 ! modified L-methionine residue is_a: MOD:00918 ! modified L-tryptophan residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00354 name: O-(riboflavin phosphoryl)-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to O-(riboflavin phosphoryl)-L-threonine." [PubMed:10587447, PubMed:11163785, PubMed:11248234, RESID:AA0349, UniMod:442] subset: PSI-MOD_slim synonym: "(R,)-2-amino-3-(riboflavin 5'-hydrogen phosphonoxy)butanoic acid" EXACT RESID-systematic [] synonym: "FMN" RELATED PSI-MS-label [] synonym: "FMN phosphoryl threonine" EXACT UniProt-feature [] synonym: "O3-(riboflavin phosphoryl)" RELATED UniMod-description [] synonym: "O3-threonyl flavin mononucleotide" EXACT RESID-alternate [] synonym: "O3-threonyl FMN" EXACT RESID-alternate [] synonym: "OFMNThr" EXACT PSI-MOD-short [] xref: DiffAvg: "438.33" xref: DiffFormula: "C 17 H 19 N 4 O 8 P 1" xref: DiffMono: "438.094050" xref: Formula: "C 21 H 26 N 5 O 10 P 1" xref: MassAvg: "539.43" xref: MassMono: "539.141729" xref: Origin: "T" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:01164 ! riboflavin-phosphoryl [Term] id: MOD:00355 name: O-(riboflavin phosphoryl)-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-(riboflavin phosphoryl)-L-serine." [RESID:AA0350, UniMod:442] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(riboflavin 5'-hydrogen phosphonoxy)propanoic acid" EXACT RESID-systematic [] synonym: "FMN" RELATED PSI-MS-label [] synonym: "FMN phosphoryl serine" EXACT UniProt-feature [] synonym: "O3-(riboflavin phosphoryl)" RELATED UniMod-description [] synonym: "O3-seryl flavin mononucleotide" EXACT RESID-alternate [] synonym: "O3-seryl FMN" EXACT RESID-alternate [] synonym: "OFMNSer" EXACT PSI-MOD-short [] xref: DiffAvg: "438.33" xref: DiffFormula: "C 17 H 19 N 4 O 8 P 1" xref: DiffMono: "438.094050" xref: Formula: "C 20 H 24 N 5 O 10 P 1" xref: MassAvg: "525.41" xref: MassMono: "525.126079" xref: Origin: "S" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01164 ! riboflavin-phosphoryl [Term] id: MOD:00356 name: S-(4a-FMN)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-(4a-FMN)-L-cysteine." [PubMed:12668455, PubMed:12846567, PubMed:7692961, RESID:AA0351, UniMod:443] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(4a-riboflavin 5'-dihydrogen phosphate)sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "4a-(S-cysteinyl)flavin mononucleotide" EXACT RESID-alternate [] synonym: "4a-(S-cysteinyl)FMN" EXACT RESID-alternate [] synonym: "FMNC" RELATED PSI-MS-label [] synonym: "S-(4a-FMN)" RELATED UniMod-description [] synonym: "S-4a-FMN cysteine" EXACT UniProt-feature [] synonym: "S4aFMNCys" EXACT PSI-MOD-short [] xref: DiffAvg: "456.34" xref: DiffFormula: "C 17 H 21 N 4 O 9 P 1 S 0" xref: DiffMono: "456.104615" xref: Formula: "C 20 H 26 N 5 O 10 P 1 S 1" xref: MassAvg: "559.49" xref: MassMono: "559.113800" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00896 ! FMN modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00357 name: 1'-(8alpha-FMN)-L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to 1'-(8alpha-FMN)-L-histidine." [PubMed:11902668, PubMed:8611516, RESID:AA0352, UniMod:409] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(1-[8alpha riboflavin 5'-dihydrogen phosphate]imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "8alpha-(N(epsilon)-histidyl)FMN" EXACT RESID-alternate [] synonym: "8alpha-(N1'-histidyl)FMN" EXACT RESID-alternate [] synonym: "flavin mononucleotide" RELATED UniMod-description [] synonym: "FMNH" RELATED PSI-MS-label [] synonym: "Ntele8aFMNHis" EXACT PSI-MOD-short [] synonym: "tau-(8alpha-FMN)-histidine" EXACT RESID-alternate [] synonym: "tele-(8alpha-FMN)-histidine" EXACT RESID-alternate [] synonym: "Tele-8alpha-FMN histidine" EXACT UniProt-feature [] xref: DiffAvg: "454.33" xref: DiffFormula: "C 17 H 19 N 4 O 9 P 1" xref: DiffMono: "454.088965" xref: Formula: "C 23 H 26 N 7 O 10 P 1" xref: MassAvg: "591.47" xref: MassMono: "591.147877" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00896 ! FMN modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00358 name: 3'-(8alpha-FMN)-L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to 3'-(8alpha-FMN)-L-histidine." [PubMed:12417325, RESID:AA0353, UniMod:409] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(3-[8alpha riboflavin 5'-dihydrogen phosphate]imidazol-4-yl)propanoic acid" EXACT RESID-systematic [] synonym: "8alpha-(N(delta)-histidyl)FMN" EXACT RESID-alternate [] synonym: "8alpha-(N3'-histidyl)FMN" EXACT RESID-alternate [] synonym: "flavin mononucleotide" RELATED UniMod-description [] synonym: "FMNH" RELATED PSI-MS-label [] synonym: "Npros8aFMNHis" EXACT PSI-MOD-short [] synonym: "pi-(8alpha-FMN)-histidine" EXACT RESID-alternate [] synonym: "pros-(8alpha-FMN)-histidine" EXACT RESID-alternate [] xref: DiffAvg: "454.33" xref: DiffFormula: "C 17 H 19 N 4 O 9 P 1" xref: DiffMono: "454.088965" xref: Formula: "C 23 H 26 N 7 O 10 P 1" xref: MassAvg: "591.47" xref: MassMono: "591.147877" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00896 ! FMN modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00359 name: N2-acetyl-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to N2-acetyl-L-arginine." [PubMed:12883043, PubMed:1894641, RESID:AA0354] subset: PSI-MOD_slim synonym: "(S)-2-acetamido-5-carbamimidamidopentanoic acid" EXACT RESID-systematic [] synonym: "2-acetamido-5-guanidinopentanoic acid" EXACT RESID-alternate [] synonym: "2-acetylamino-5-guanidinopentanoic acid" EXACT RESID-alternate [] synonym: "AcArg" EXACT PSI-MOD-short [] synonym: "acetylarginine" EXACT RESID-alternate [] synonym: "alpha-acetylamino-delta-guanidinovaleric acid" EXACT RESID-alternate [] synonym: "N(alpha)-acetylarginine" EXACT RESID-alternate [] synonym: "N2-acetylarginine" EXACT UniProt-feature [] synonym: "N2-acetylated L-arginine" EXACT PSI-MOD-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 8 H 15 N 4 O 2" xref: MassAvg: "199.23" xref: MassMono: "199.119501" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00360 name: L-cysteinyl copper sulfido molybdopterin cytosine dinuncleotide namespace: PSI-MOD def: "modification from RESID" [PubMed:12475995, RESID:AA0355, UniMod:444] subset: PSI-MOD_slim synonym: "[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with cytosine)methyl-6-oxo-3,4-dimercapto-pteridino[6,7-5,6]pyranoato-S3,S4]-cysteinyl-S-copper-mu-sulfido-molybdenum hydroxide oxide" EXACT RESID-systematic [] synonym: "copper sulfido molybdopterin cytosine dinuncleotide" RELATED UniMod-description [] synonym: "CuSMo" RELATED PSI-MS-label [] synonym: "cysteinyl copper mu-sulfido Mo-pterin cytosine dinucleotide" EXACT RESID-alternate [] xref: DiffAvg: "922.09" xref: DiffFormula: "C 19 Cu 1 H 24 Mo 1 N 8 O 15 P 2 S 3" xref: DiffMono: "922.834854" xref: Formula: "C 22 Cu 1 H 29 Mo 1 N 9 O 16 P 2 S 4" xref: MassAvg: "1025.23" xref: MassMono: "1025.844039" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00742 ! copper containing modified residue is_a: MOD:00744 ! molybdenum pterin containing modification is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00361 name: tris-L-cysteinyl S-adenosylmethion-N,O-diyl tetrairon tetrasulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:11222759, PubMed:14704425, RESID:AA0356] comment: Cross-link 3. subset: PSI-MOD_slim synonym: "tetra-mu3-sulfido(S-adenosylmethion-N,O-diyliron)tris(S-cysteinyliron)" EXACT RESID-systematic [] xref: DiffAvg: "747.05" xref: DiffFormula: "C 15 Fe 4 H 19 N 6 O 5 S 5" xref: DiffMono: "746.741798" xref: FormalCharge: "1+" xref: Formula: "C 24 Fe 4 H 34 N 9 O 8 S 8" xref: MassAvg: "1056.48" xref: MassMono: "1055.768803" xref: Origin: "C, C, C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00362 name: tris-L-cysteinyl L-arginyl diiron disulfide namespace: PSI-MOD def: "modification from RESID" [PubMed:14704425, RESID:AA0357] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "di-mu-sulfido(N(eta1)-arginyl-S-cysteinyliron)(bis-S-cysteinyliron)" EXACT RESID-systematic [] xref: DiffAvg: "172.80" xref: DiffFormula: "C 0 Fe 2 H -3 N 0 O 0 S 2" xref: DiffMono: "172.790542" xref: Formula: "C 15 Fe 2 H 24 N 7 O 4 S 5" xref: MassAvg: "638.41" xref: MassMono: "637.919207" xref: Origin: "C, C, C, R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00902 ! modified L-arginine residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00363 name: L-cysteinyl-L-selenocysteine (Cys-Sec) namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-selenocysteine residues to form L-cysteinyl-L-selenocystine." [PubMed:12911312, RESID:AA0358] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R,R)-2-amino-3-[3-(2-aminopropanoic acid)sulfanyl]selanylpropanoic acid" EXACT RESID-systematic [] synonym: "Cysteinyl-selenocysteine (Sec-Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0 Se 0" xref: DiffMono: "-2.015650" xref: Formula: "C 6 H 8 N 2 O 2 S 1 Se 1" xref: MassAvg: "251.16" xref: MassMono: "251.947170" xref: Origin: "C, U" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01158 ! modified L-selenocysteine residue [Term] id: MOD:00364 name: 5-hydroxy-N6,N6,N6-trimethyl-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to 5-hydroxy-N6,N6,N6-trimethyl-L-lysine." [PubMed:11349130, PubMed:14661085, RESID:AA0359, UniMod:445] comment: Incidental to RESID:AA0278; secondary to RESID:AA0028; secondary to RESID:AA0074. subset: PSI-MOD_slim synonym: "(2S,5Xi)-2-amino-5-hydroxy-6-(trimethylammonio)hexanoic acid" EXACT RESID-systematic [] synonym: "(2Xi,5S)-5-amino-5-carboxy-2-hydroxy-N,N,N-trimethylpentanaminium" EXACT RESID-alternate [] synonym: "5-hydroxy-N(zeta)-trimethyllysine" EXACT RESID-alternate [] synonym: "5-hydroxy-N6,N6,N6-trimethyl" RELATED UniMod-description [] synonym: "5-hydroxylated N6,N6,N6-trimethylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "5HyN6Me3Lys" EXACT PSI-MOD-short [] synonym: "alpha-amino-epsilon-dimethylamino-delta-hydroxycaproic acid" EXACT RESID-alternate [] synonym: "delta-hydroxy-epsilon-N,N,N-trimethyllysine" EXACT RESID-alternate [] synonym: "Hydroxytrimethyl" RELATED PSI-MS-label [] synonym: "lysine derivative Lys(z)" EXACT RESID-alternate [] synonym: "N6,N6,N6-trimethyl-5-hydroxylysine" EXACT UniProt-feature [] xref: DiffAvg: "59.09" xref: DiffFormula: "C 3 H 7 N 0 O 1" xref: DiffMono: "59.049690" xref: FormalCharge: "1+" xref: Formula: "C 9 H 19 N 2 O 2" xref: MassAvg: "187.26" xref: MassMono: "187.144104" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00602 ! N-methylated residue is_a: MOD:00912 ! modified L-lysine residue relationship: has_functional_parent MOD:00037 ! 5-hydroxy-L-lysine relationship: has_functional_parent MOD:00083 ! N6,N6,N6-trimethyl-L-lysine [Term] id: MOD:00365 name: N-(L-isoglutamyl)-glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-glutamic acid residue and a glycine residue by an isopeptide bond to form N-(L-isoglutamyl)-glycine." [PubMed:14531691, RESID:AA0360] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S)-2-amino-5-(carboxymethyl)amino-5-oxopentanoic acid" EXACT RESID-systematic [] synonym: "2-amino-N5-(carboxymethyl)-pentanediamic acid" EXACT RESID-alternate [] synonym: "isoglutamyl glycine" EXACT RESID-alternate [] synonym: "Isoglutamyl glycine isopeptide (Gly-Glu)" EXACT UniProt-feature [] synonym: "N-gamma-glutamylglycine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 7 H 9 N 2 O 3" xref: MassAvg: "169.16" xref: MassMono: "169.061317" xref: Origin: "E, G" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00688 ! isopeptide crosslinked residues is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00908 ! modified glycine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00366 name: O-sulfo-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-sulfo-L-serine." [PubMed:14752058, RESID:AA0361, UniMod:40] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-hydroxypropanoic acid 3-sulfate" EXACT RESID-systematic [] synonym: "O-Sulfonation" RELATED UniMod-description [] synonym: "O3-sulfonoserine" EXACT RESID-alternate [] synonym: "O3-sulfoserine" EXACT RESID-alternate [] synonym: "serine sulfate ester" EXACT RESID-alternate [] synonym: "Sulfo" RELATED PSI-MS-label [] synonym: "Sulfoserine" EXACT UniProt-feature [] xref: DiffAvg: "80.06" xref: DiffFormula: "C 0 H 0 N 0 O 3 S 1" xref: DiffMono: "79.956815" xref: Formula: "C 3 H 5 N 1 O 5 S 1" xref: MassAvg: "167.14" xref: MassMono: "166.988843" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00695 ! sulfated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00367 name: O-sulfo-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to O-sulfo-L-threonine." [PubMed:14752058, RESID:AA0362, UniMod:40] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-hydroxybutanoic acid 3-sulfate" EXACT RESID-systematic [] synonym: "O-Sulfonation" RELATED UniMod-description [] synonym: "O3-sulfonothreonine" EXACT RESID-alternate [] synonym: "O3-sulfothreonine" EXACT RESID-alternate [] synonym: "Sulfo" RELATED PSI-MS-label [] synonym: "Sulfothreonine " EXACT UniProt-feature [] synonym: "threonine sulfate ester" EXACT RESID-alternate [] xref: DiffAvg: "80.06" xref: DiffFormula: "C 0 H 0 N 0 O 3 S 1" xref: DiffMono: "79.956815" xref: Formula: "C 4 H 7 N 1 O 5 S 1" xref: MassAvg: "181.17" xref: MassMono: "181.004493" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00695 ! sulfated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00368 name: N-carboxy-L-methionine namespace: PSI-MOD def: "A protein modification that effectively converts an L-methionine residue to N-carboxy-L-methionine." [PubMed:10368287, PubMed:11120890, PubMed:12595263, PubMed:8312270, RESID:AA0363, UniMod:299] subset: PSI-MOD_slim synonym: "(S)-2-carboxyamino-4-(methylsulfanyl)butanoic acid" EXACT RESID-systematic [] synonym: "2-carbamic-4-(methylsulfanyl)butanoic acid" EXACT RESID-alternate [] synonym: "2-carbamic-4-(methylthio)butanoic acid" EXACT RESID-alternate [] synonym: "Carboxy" RELATED UniMod-interim [] synonym: "Carboxylation" RELATED UniMod-description [] synonym: "N-carboxymethionine" EXACT RESID-alternate [] xref: DiffAvg: "44.01" xref: DiffFormula: "C 1 H 0 N 0 O 2 S 0" xref: DiffMono: "43.989829" xref: Formula: "C 6 H 10 N 1 O 3 S 1" xref: MassAvg: "176.21" xref: MassMono: "176.038139" xref: Origin: "M" xref: Source: "hypothetical" xref: TermSpec: "N-term" is_a: MOD:00913 ! modified L-methionine residue is_a: MOD:01152 ! carboxylated residue [Term] id: MOD:00369 name: O-acetyl-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-acetyl-L-serine." [ChEBI:17981, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, PubMed:16731519, PubMed:489587, PubMed:7309355, RESID:AA0364, UniMod:1] comment: incidental to RESID:AA0051 subset: PSI-MOD_slim synonym: "(S)-2-amino-3-acetyloxypropanoic acid" EXACT RESID-systematic [] synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "Acetylation" RELATED UniMod-description [] synonym: "O-acetylated L-serine" EXACT PSI-MOD-alternate [] synonym: "O-acetylserine" EXACT UniProt-feature [] synonym: "O-acetylserine" EXACT RESID-alternate [] synonym: "OAcSer" EXACT PSI-MOD-short [] synonym: "serine acetate ester" EXACT RESID-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 5 H 7 N 1 O 3" xref: MassAvg: "129.11" xref: MassMono: "129.042593" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00644 ! O-acetylated residue is_a: MOD:00647 ! acetylated L-serine [Term] id: MOD:00370 name: (E)-2,3-didehydrotyrosine namespace: PSI-MOD def: "A protein modification that effectively converts L-tyrosine to (E)-2,3-didehydrotyrosine." [PubMed:12623015, RESID:AA0365, UniMod:401] comment: incidental to RESID:AA0184; incidental to RESID:AA0187; incidental to RESID:AA0188; incidental to RESID:AA0189; incidental to RESID:AA0378; incidental to RESID:AA0379; incidental to RESID:AA0380; incidental to RESID:AA0381 subset: PSI-MOD_slim synonym: "(E)-2,3-didehydrogenated tyrosine" EXACT PSI-MOD-alternate [] synonym: "(E)-2,3-didehydrotyrosine" EXACT UniProt-feature [] synonym: "(E)-2-amino-3-(4-hydoxyphenyl)propenoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-oxo-butanoic_acid" RELATED UniMod-description [] synonym: "amino-(para-hydroxybenzylidenyl)acetic acid" EXACT RESID-alternate [] synonym: "blue non-fluorescent pocilloporin chromophore" EXACT RESID-alternate [] synonym: "Didehydro" RELATED PSI-MS-label [] synonym: "E-dHTyr" EXACT PSI-MOD-short [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] synonym: "trans-dehydrotyrosine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" xref: Formula: "C 9 H 7 N 1 O 2" xref: MassAvg: "161.16" xref: MassMono: "161.047678" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00706 ! dehydrogenated tyrosine [Term] id: MOD:00371 name: bis-L-aspartato tris-L-glutamato L-histidino calcium tetramanganese tetroxide namespace: PSI-MOD def: "modification from RESID" [PubMed:14764885, RESID:AA0366] comment: Cross-link 6. subset: PSI-MOD_slim synonym: "4Mn-Ca-4O cluster" EXACT RESID-alternate [] synonym: "mu3-1:2:3kappaO-oxido-mu3-1:3:4kappaO-oxido-mu3-2:3:4kappaO-oxido-mu4-1:2:4:5kappaO-oxido-N1'-histidino-O5-glutamato 2-manganese-O5,O5-glutamato 3-manganese-O4-aspartato 4-manganese-O4-aspartato-O5-glutamato 5-manganese" EXACT RESID-systematic [] synonym: "photosystem II catalytic cluster" EXACT RESID-alternate [] xref: DiffAvg: "317.78" xref: DiffFormula: "C 0 Ca 1 H -6 Mn 4 N 0 O 4" xref: DiffMono: "317.647480" xref: Formula: "C 29 Ca 1 H 32 Mn 4 N 8 O 20" xref: MassAvg: "1072.44" xref: MassMono: "1071.888057" xref: Origin: "D, D, E, E, E, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00740 ! manganese containing modified residue is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01482 ! calcium containing modified residue [Term] id: MOD:00372 name: 3'-(3'-L-tyrosinyl)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively cross-links L-tyrosine residues to form 3'-(3'-L-tyrosinyl)-L-tyrosine." [DeltaMass:0, PubMed:14249161, PubMed:637884, PubMed:8702710, PubMed:8937563, RESID:AA0367] comment: Cross-link 2; From DeltaMass: Average Mass: -2. subset: PSI-MOD_slim synonym: "(2S,2'S)-3,3'-(6,6'-dihydroxybiphenyl-3,3'-diyl)bis(2-aminopropanoic acid)" EXACT RESID-systematic [] synonym: "3,3'-BiTyr (Crosslink)" EXACT DeltaMass-label [] synonym: "6,6'-dihydroxy-(1,1'-biphenyl)-3,3'-bis(2-aminopropanoic acid)" EXACT RESID-alternate [] synonym: "alpha,alpha'-diamino-6,6'-dihydroxy-(1,1'-biphenyl)-3,3'-dipropanoic acid" EXACT RESID-alternate [] synonym: "bityrosine" EXACT RESID-alternate [] synonym: "o,o-dityrosine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" xref: Formula: "C 18 H 16 N 2 O 4" xref: MassAvg: "324.33" xref: MassMono: "324.111007" xref: Origin: "Y, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00373 name: 3'-(O4'-L-tyrosinyl)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively cross-links L-tyrosine residues with an ether bond to form 3'-(O4'-L-tyrosinyl)-L-tyrosine," [DeltaMass:0, PubMed:12719529, PubMed:7115340, PubMed:8702710, RESID:AA0368] comment: Cross-link 2; secondary to RESID:AA0146; From DeltaMass: Average Mass: -2. subset: PSI-MOD_slim synonym: "(2S)-2-amino-3-[3-(4-[(2S)-2-amino-2-carboxyethyl]phenoxy)-4-hydroxyphenyl]propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-[4-(5-[(2S)-2-amino-2-carboxyethyl]-2-hydroxyphenoxy)phenyl]propanoic acid" EXACT RESID-alternate [] synonym: "IsodiTyr (Crosslink)" EXACT DeltaMass-label [] synonym: "isodityrosine" EXACT RESID-alternate [] synonym: "Isodityrosine (Tyr-Tyr)" EXACT UniProt-feature [] synonym: "O-(5-(2-amino-2-carboxyethyl)-2-hydroxyphenyl)-L-tyrosine" EXACT RESID-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" xref: Formula: "C 18 H 16 N 2 O 4" xref: MassAvg: "324.33" xref: MassMono: "324.111007" xref: Origin: "Y, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00374 name: 3,4-dihydroxy-L-arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to 3,4-dihydroxy-L-arginine." [PubMed:10978343, PubMed:12686488, RESID:AA0369, UniMod:425] subset: PSI-MOD_slim synonym: "(2S,3Xi,4Xi)-2-amino-5-carbamimidamido-3,4-dihydroxypentanoic acid" EXACT RESID-systematic [] synonym: "2-amino-5-guanidino-3,4-dihydroxypentanoic acid" EXACT RESID-alternate [] synonym: "3,4-dihydroxyarginine" EXACT UniProt-feature [] synonym: "3,4-dihydroxylated L-arginine" EXACT PSI-MOD-alternate [] synonym: "34Hy2Arg" EXACT PSI-MOD-short [] synonym: "beta,gamma-dihydroxyarginine" EXACT RESID-alternate [] synonym: "dihydroxy" RELATED UniMod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2" xref: DiffMono: "31.989829" xref: Formula: "C 6 H 12 N 4 O 3" xref: MassAvg: "188.18" xref: MassMono: "188.090940" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00682 ! hydroxylated arginine [Term] id: MOD:00375 name: 4,5-dihydroxy-L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to 4,5-dihydroxy-L-lysine." [PubMed:10978343, PubMed:12686488, RESID:AA0370, UniMod:425] subset: PSI-MOD_slim synonym: "(2S,4Xi,5Xi)-2,6-diamino-4,5-dihydroxyhexanoic acid" EXACT RESID-systematic [] synonym: "4,5-dihydroxylated L-lysine" EXACT PSI-MOD-alternate [] synonym: "4,5-dihydroxylysine" EXACT UniProt-feature [] synonym: "45Hy2Lys" EXACT PSI-MOD-short [] synonym: "alpha,epsilon-diamino-delta,gamma-dihydroxycaproic acid" EXACT RESID-alternate [] synonym: "delta,gamma-dihydroxylysine" EXACT RESID-alternate [] synonym: "dihydroxy" RELATED UniMod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2" xref: DiffMono: "31.989829" xref: Formula: "C 6 H 12 N 2 O 3" xref: MassAvg: "160.17" xref: MassMono: "160.084792" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00681 ! hydroxylated lysine [Term] id: MOD:00376 name: 1'-(phospho-5'-adenosine)-L-histidine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-histidine residue and 5'-phosphoadenosine through a phosphoramide ester bond to form 1'-(phospho-5'-adenosine)-L-histidine." [PubMed:15182206, PubMed:9323207, RESID:AA0371, UniMod:405] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[1-(5'-adenosine phosphono)imidazol-4-yl]propanoic acid" EXACT RESID-systematic [] synonym: "AMP binding site" RELATED UniMod-description [] synonym: "L-histidine 5'-adenosine phosphoramidester" EXACT RESID-alternate [] synonym: "L-histidine monoanhydride with 5'-adenylic acid" EXACT RESID-alternate [] synonym: "N1'-adenylylated histidine" EXACT RESID-alternate [] synonym: "Phosphoadenosine" RELATED PSI-MS-label [] synonym: "tau-5'-adenylic-L-histidine" EXACT RESID-alternate [] synonym: "tele-5'-adenylic-L-histidine" EXACT RESID-alternate [] xref: DiffAvg: "329.21" xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1" xref: DiffMono: "329.052520" xref: Formula: "C 16 H 19 N 8 O 7 P 1" xref: MassAvg: "466.35" xref: MassMono: "466.111432" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01165 ! adenylated residue [Term] id: MOD:00377 name: 1'-(phospho-5'-uridine)-L-histidine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-histidine residue and 5'-phosphouridine through a phosphoramide ester bond to form 1'-(phospho-5'-uridine)-L-histidine." [PubMed:11467524, PubMed:321007, PubMed:380639, PubMed:8794735, RESID:AA0372, UniMod:417] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[1-(5'-uridine phosphono)imidazol-4-yl]propanoic acid" EXACT RESID-systematic [] synonym: "L-histidine 5'-uridine phosphoramidester" EXACT RESID-alternate [] synonym: "L-histidine monoanhydride with 5'-uridylic acid" EXACT RESID-alternate [] synonym: "N1'-uridylylated histidine" EXACT RESID-alternate [] synonym: "PhosphoUridine" RELATED PSI-MS-label [] synonym: "tau-5'-uridylic-L-histidine" EXACT RESID-alternate [] synonym: "tele-5'-uridylic-L-histidine" EXACT RESID-alternate [] synonym: "uridine phosphodiester" RELATED UniMod-description [] xref: DiffAvg: "306.17" xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1" xref: DiffMono: "306.025302" xref: Formula: "C 15 H 18 N 5 O 9 P 1" xref: MassAvg: "443.31" xref: MassMono: "443.084214" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00909 ! modified L-histidine residue is_a: MOD:01166 ! uridylated residue [Term] id: MOD:00378 name: L-aspartyl aldehyde namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartyl aldehyde." [PubMed:1093385, PubMed:14235557, PubMed:15237995, RESID:AA0373, UniMod:447] subset: PSI-MOD_slim synonym: "(S)-2-amino-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "Aspartyl aldehyde" EXACT UniProt-feature [] synonym: "Deoxy" RELATED PSI-MS-label [] synonym: "L-aminosuccinaldehydic acid" EXACT RESID-alternate [] synonym: "L-aminosuccinic acid semialdehyde" EXACT RESID-alternate [] synonym: "L-aspartate-beta-semialdehyde" EXACT RESID-alternate [] synonym: "L-aspartic beta-semialdehyde" EXACT RESID-alternate [] synonym: "L-beta-formylalanine" EXACT RESID-alternate [] synonym: "reduction" RELATED UniMod-description [] xref: DiffAvg: "-16.00" xref: DiffFormula: "C 0 H 0 N 0 O -1" xref: DiffMono: "-15.994915" xref: Formula: "C 4 H 5 N 1 O 2" xref: MassAvg: "99.09" xref: MassMono: "99.032028" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01161 ! deoxygenated residue [Term] id: MOD:00379 name: L-serine microcin E492 siderophore ester namespace: PSI-MOD def: "modification from RESID" [PubMed:15102848, RESID:AA0374, UniMod:448] comment: UniMod origin corrected. [JSG] subset: PSI-MOD_slim synonym: "Microcin" RELATED PSI-MS-label [] synonym: "microcin E492 siderophore ester from serine" RELATED UniMod-description [] synonym: "N-[5-(6-O-seryl-beta-glucosyl)-2,3-dihydroxybenzoyl]-O-[N-(2,3-dihydroxybenzoyl)-O-[N-(2,3-dihydroxybenzoyl)seryl]seryl]serine" EXACT RESID-systematic [] synonym: "Serine microcin E492 siderophore ester" EXACT UniProt-feature [] xref: DiffAvg: "831.69" xref: DiffFormula: "C 36 H 37 N 3 O 20" xref: DiffMono: "831.197041" xref: Formula: "C 39 H 43 N 4 O 23" xref: MassAvg: "935.77" xref: MassMono: "935.231809" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00380 name: L-aspartyl molybdenum bis(molybdopterin guanine dinucleotide) namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to L-aspartyl molybdenum bis(molybdopterin guanine dinucleotide)." [PubMed:12910261, PubMed:14725769, RESID:AA0375, UniMod:424] subset: PSI-MOD_slim synonym: "2-amino-5,6-dimercapto-7-methyl-3,7,8a,9-tetrahydro-8-oxa-1,3,9,10-tetraazaanthracen-4-one guanosine dinucleotide" EXACT RESID-alternate [] synonym: "bis[8-amino-1a,2,4a,5,6,7,10-heptahydro-2-(trihydrogen diphosphate 5'-ester with guanosine)methyl-6-oxo-3,4-disulfanyl-pteridino[6,7-5,6]pyranoato-S3,S4]-aspartyl-molybdenum" EXACT RESID-systematic [] synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED UniMod-description [] synonym: "MolybdopterinGD" RELATED PSI-MS-label [] synonym: "nitrate reductase A aspartyl Mo-bisMGD cofactor" EXACT RESID-alternate [] synonym: "phosphoric acid 4-(2-amino-4-oxo-3,4,5,6,-tetrahydro-pteridin-6-yl)-2-hydroxy-3,4-dimercapto-but-3-en-yl ester guanylate ester" EXACT RESID-alternate [] xref: DiffAvg: "1572.03" xref: DiffFormula: "C 40 H 47 Mo 1 N 20 O 26 P 4 S 4" xref: DiffMono: "1572.985775" xref: Formula: "C 44 H 52 Mo 1 N 21 O 29 P 4 S 4" xref: MassAvg: "1687.12" xref: MassMono: "1688.012718" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:01167 ! molybdopterin guanine dinucleotide [Term] id: MOD:00382 name: 3-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-one namespace: PSI-MOD def: "modification from RESID" [PubMed:10852900, PubMed:11259412, PubMed:15491166, RESID:AA0377] comment: carboxamidine; cross-link 1 subset: PSI-MOD_slim synonym: "3-(2-methylsulfanyl)ethyl-6-(4-hydroxybenzylidene)-5-iminopiperazin-2-one" EXACT RESID-systematic [] synonym: "3-(2-methylthio)ethyl-6-(4-hydroxybenzylidene)-5-amino-3,6-didehydropyrazin-2-ol" EXACT RESID-alternate [] synonym: "GFP-like chromoprotein asFP595 chromophore" EXACT RESID-alternate [] synonym: "L-methionyl-L-tyrosyl-2-keto-5-iminopiperazine" EXACT RESID-alternate [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1 S 0" xref: DiffMono: "-20.026215" xref: Formula: "C 14 H 15 N 2 O 2 S 1" xref: MassAvg: "275.35" xref: MassMono: "275.085424" xref: Origin: "G, M" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00913 ! modified L-methionine residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00383 name: 2-imino-glutamic acid 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-glutamic acid residue and a glycine residue to form 2-imino-glutamic acid 5-imidazolinone glycine." [PubMed:11682051, RESID:AA0378] comment: Cross-link 2; carboxamidine; cross-link 1; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "2,N-didehydroglutamyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "2-(3-carboxy-1-iminopropyl)-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "2-imino-glutamyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "2-iminomethyl-5-imidazolinone (Glu-Gly)" EXACT UniProt-feature [] synonym: "[2-(3-carboxy-1-iminopropyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1" xref: DiffMono: "-20.026215" xref: Formula: "C 7 H 6 N 2 O 3" xref: MassAvg: "166.13" xref: MassMono: "166.037842" xref: Origin: "E, G" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00384 name: 2-imino-methionine 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-methionine residue and a glycine residue to form 2-imino-methionine 5-imidazolinone glycine." [PubMed:10852900, PubMed:12185250, PubMed:12909624, PubMed:15542608, RESID:AA0379] comment: Cross-link 2; carboxamidine; cross-link 1; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "(2-[1-imino-3-(methylsulfanyl)propyl]-5-oxo-4,5-dihydro-imidazol-1-yl)acetic acid" EXACT RESID-alternate [] synonym: "2,N-didehydromethionyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "2-[1-imino-3-(methylsulfanyl)propyl]-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "2-imino-methionyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "2-iminomethyl-5-imidazolinone (Met-Gly)" EXACT UniProt-feature [] synonym: "GFP-like chromoprotein asFP595 chromophore" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] synonym: "red fluorescent protein eqFP611 chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-20.03" xref: DiffFormula: "C 0 H -4 N 0 O -1 S 0" xref: DiffMono: "-20.026215" xref: Formula: "C 7 H 8 N 2 O 1 S 1" xref: MassAvg: "168.22" xref: MassMono: "168.035734" xref: Origin: "G, M" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00908 ! modified glycine residue is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00385 name: L-asparagine 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-asparagine residue and a glycine residue to form L-asparagine 5-imidazolinone glycine." [PubMed:10504696, RESID:AA0380] comment: Cross-link 2; carboxamidine; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "2-[(S)-1,3-diamino-3-oxopropyl]-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "5-imidazolinone (Asn-Gly)" EXACT UniProt-feature [] synonym: "[2-(1,3-diamino-3-oxopropyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid" EXACT RESID-alternate [] synonym: "asparaginyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] synonym: "Zoanthus sp. fluorescent protein FP506 chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 6 H 7 N 3 O 2" xref: MassAvg: "153.14" xref: MassMono: "153.053826" xref: Origin: "G, N" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00903 ! modified L-asparagine residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00386 name: L-lysine 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-lysine residue and a glycine residue to form L-lysine 5-imidazolinone glycine." [PubMed:10504696, RESID:AA0381] comment: Cross-link 2; carboxamidine; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "2-[(S)-1,5-diaminopentanyl]-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "5-imidazolinone (Lys-Gly)" EXACT UniProt-feature [] synonym: "[2-(1,5-diaminopentanyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid" EXACT RESID-alternate [] synonym: "Anemonia majano fluorescent protein FP486 chromophore" EXACT RESID-alternate [] synonym: "lysyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 8 H 13 N 3 O 1" xref: MassAvg: "167.21" xref: MassMono: "167.105862" xref: Origin: "G, K" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00908 ! modified glycine residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00387 name: 2-tetrahydropyridinyl-5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-lysine residue and a glycine residue to form 2-tetrahydropyridinyl-5-imidazolinone glycine." [PubMed:10504696, PubMed:15628861, RESID:AA0382] comment: Cross-link 2; carboxamidine; incidental to RESID:AA0183; incidental to RESID:AA0365. subset: PSI-MOD_slim synonym: "2-(3,4,5,6-tetrahydropyridin-2-yl)-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "2-(tetrahydropyrid-2-yl)-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "2-tetrahydro-2-pyridyl-5-imidazolinone (Lys-Gly)" EXACT UniProt-feature [] synonym: "[5-oxo-2-(3,4,5,6-tetrahydropyridin-2-yl)-4,5-dihydro-1H-imidazol-1-yl]acetic acid" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] synonym: "Zoanthus sp. fluorescent protein zFP538 chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-37.06" xref: DiffFormula: "C 0 H -7 N -1 O -1" xref: DiffMono: "-37.052764" xref: Formula: "C 8 H 9 N 2 O 1" xref: MassAvg: "149.17" xref: MassMono: "149.071488" xref: Origin: "G, K" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00908 ! modified glycine residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00388 name: L-alanyl-pentaglycyl-murein peptidoglycan namespace: PSI-MOD def: "modification from RESID" [PubMed:8163519, RESID:AA0383] subset: PSI-MOD_slim synonym: "(2R,6S)-2-(N-mureinyl-(R)-alanyl-(S)-isoglutamyl)amino-6-(alanyl-pentaglycyl)amino-pimeloyl-(S)-alanyl-(S)-alanine" EXACT RESID-alternate [] synonym: "Pentaglycyl murein peptidoglycan amidated alanine" EXACT UniProt-feature [] xref: DiffAvg: "268.25" xref: DiffFormula: "C 10 H 14 N 5 O 4" xref: DiffMono: "268.104579" xref: Formula: "C 13 H 20 N 6 O 6" xref: MassAvg: "356.33" xref: MassMono: "356.144432" xref: Origin: "A" xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00901 ! modified L-alanine residue is_a: MOD:01159 ! peptidoglycanated residue [Term] id: MOD:00389 name: N-formyl-L-proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to N-formyl-L-proline." [PubMed:12051774, PubMed:5464655, RESID:AA0384] comment: CAUTION - observations of this modification can be attributed to unintended artifactual production, or to spurious peptide MS identification. This modification is probably not a natural post-translational modification [JSG]. subset: PSI-MOD_slim synonym: "(S)-1-formyl-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] synonym: "1-formylproline" EXACT RESID-alternate [] synonym: "1-formylpyrrolidine-2-carboxylic acid" EXACT RESID-alternate [] synonym: "N-formylated L-proline" EXACT PSI-MOD-alternate [] synonym: "NFoPro" EXACT PSI-MOD-short [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 H 0 N 0 O 1" xref: DiffMono: "27.994915" xref: Formula: "C 6 H 8 N 1 O 2" xref: MassAvg: "126.13" xref: MassMono: "126.055504" xref: Origin: "P" xref: Source: "hypothetical" xref: TermSpec: "N-term" is_a: MOD:00409 ! N-formylated residue is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00390 name: O-decanoyl-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to O-decanoyl-L-serine." [PubMed:12630926, RESID:AA0385, UniMod:449] subset: PSI-MOD_slim synonym: "(2S)-2-amino-3-(decanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "Decanoyl" RELATED PSI-MS-label [] synonym: "L-serine decanoate ester" EXACT RESID-alternate [] synonym: "lipid" RELATED UniMod-description [] synonym: "O-decanoyl serine" EXACT UniProt-feature [] synonym: "O-decanoylated L-serine" EXACT PSI-MOD-alternate [] synonym: "O3-decanoyl-L-serine" EXACT RESID-alternate [] synonym: "ODecSer" EXACT PSI-MOD-short [] xref: DiffAvg: "154.25" xref: DiffFormula: "C 10 H 18 N 0 O 1" xref: DiffMono: "154.135765" xref: Formula: "C 13 H 23 N 1 O 3" xref: MassAvg: "241.33" xref: MassMono: "241.167794" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00668 ! O-decanoylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00391 name: O-octanoyl-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to O-octanoyl-L-threonine." [PubMed:11546772, PubMed:12716131, RESID:AA0386, UniMod:426] subset: PSI-MOD_slim synonym: "(2S)-2-amino-3-(octanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "L-threonine octanoate ester" EXACT RESID-alternate [] synonym: "O-octanoyl threonine" EXACT UniProt-feature [] synonym: "O-octanoylated L-threonine" EXACT PSI-MOD-alternate [] synonym: "O3-octanoyl-L-threonine" EXACT RESID-alternate [] synonym: "Octanoyl" RELATED PSI-MS-label [] synonym: "octanoyl" RELATED UniMod-description [] synonym: "OOctThr" EXACT PSI-MOD-short [] xref: DiffAvg: "126.20" xref: DiffFormula: "C 8 H 14 N 0 O 1" xref: DiffMono: "126.104465" xref: Formula: "C 12 H 21 N 1 O 3" xref: MassAvg: "227.30" xref: MassMono: "227.152144" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00669 ! O-octanoylated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00392 name: O-decanoyl-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to O-decanoyl-L-threonine." [PubMed:11546772, RESID:AA0387, UniMod:449] subset: PSI-MOD_slim synonym: "(2S)-2-amino-3-(decanoyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "Decanoyl" RELATED PSI-MS-label [] synonym: "L-threonine decanoate ester" EXACT RESID-alternate [] synonym: "lipid" RELATED UniMod-description [] synonym: "O-decanoyl threonine" EXACT UniProt-feature [] synonym: "O-decanoylated L-threonine" EXACT PSI-MOD-alternate [] synonym: "O3-decanoyl-L-threonine" EXACT RESID-alternate [] synonym: "ODecThr" EXACT PSI-MOD-short [] xref: DiffAvg: "154.25" xref: DiffFormula: "C 10 H 18 N 0 O 1" xref: DiffMono: "154.135765" xref: Formula: "C 14 H 25 N 1 O 3" xref: MassAvg: "255.35" xref: MassMono: "255.183444" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00668 ! O-decanoylated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00393 name: O-methylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydroxyl group hydrogen with a methyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OMeRes" EXACT PSI-MOD-short [] is_a: MOD:00427 ! methylated residue [Term] id: MOD:00394 name: acetylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with an acetyl group." [DeltaMass:0, PubMed:11857757, PubMed:11999733, PubMed:12175151, PubMed:14730666, PubMed:15350136, UniMod:1] comment: Amino hydrogens are replaced to produce amides; hydroxyl hydrogens are replaced to produce esters; and hydrosulfanyl (thiol) hydrogens are replaced to produce sulfanyl esters (thiol esters). From DeltaMass: Average Mass: 42 subset: PSI-MOD_slim synonym: "Acetyl" RELATED PSI-MS-label [] synonym: "Acetylation" RELATED UniMod-description [] synonym: "Acetylation (N terminus, N epsilon of Lysine, O of Serine) (Ac)" EXACT DeltaMass-label [] synonym: "AcRes" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 O 1" xref: DiffMono: "42.010565" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00649 ! acylated residue [Term] id: MOD:00395 name: thioester crosslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two residues by formation of a thioester bond between a cysteine thiol and either an alpha-carbonyl, as in S-(L-methionyl-L-cysteine), or a sidechain carbonyl, as in S-(L-isoglutamyl)-L-cysteine." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00396 name: O-glycosylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces a residue hydrogen atom on an oxygen with a carbohydrate-like group through a glycosidic bond" [PubMed:18688235] subset: PSI-MOD_slim synonym: "OGlycoRes" EXACT PSI-MOD-short [] is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00398 name: carbamylated residue by cyanate or urea derivatization namespace: PSI-MOD def: "A protein modification that is produced by hydrogen cyanate, as a reagent or as released by urea degradation, reaction with a reactive hydrogen to form a carbamyl group or, in the case of an amine, to form a ureido group." [DeltaMass:56, PubMed:10978403, PubMed:12203680, UniMod:5] comment: From DeltaMass: Average Mass: 43 Formula: -NH2 to -NHCONH2 Monoisotopic Mass Change:43.006 Average Mass Change: 43.025 Notes: Generally the result of the reaction of cyanate (from sources such as old or impure urea) with primary amines. Cyanylated lysine is no longer a substrate for trypsin. subset: PSI-MOD_slim synonym: "Carbamyl" RELATED UniMod-interim [] synonym: "Carbamylation" EXACT DeltaMass-label [] synonym: "Carbamylation" RELATED UniMod-description [] xref: DiffAvg: "43.02" xref: DiffFormula: "C 1 H 1 N 1 O 1" xref: DiffMono: "43.005814" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "N-term" is_a: MOD:00848 ! reagent derivatized residue [Term] id: MOD:00400 name: deamidated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a carboxamido group with a carboxyl group, with both a gain of oxygen and a loss of nitrogen." [DeltaMass:32, UniMod:7] comment: From DeltaMass: References:Vish Katta. subset: PSI-MOD_slim synonym: "Deamidated" RELATED UniMod-interim [] synonym: "Deamidation" RELATED UniMod-description [] synonym: "Deamidation of Asparagine and Glutamine to Aspartate and Glutamate" EXACT DeltaMass-label [] synonym: "dNRes" EXACT PSI-MOD-short [] xref: DiffAvg: "0.98" xref: DiffFormula: "H -1 N -1 O 1" xref: DiffMono: "0.984016" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00408 name: N-acetylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue amino or imino hydrogen with an acetyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "N-Acetyl" EXACT PSI-MOD-alternate [] synonym: "N-Acetylation" EXACT PSI-MOD-alternate [] synonym: "NAcRes" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 O 1" xref: DiffMono: "42.010565" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00394 ! acetylated residue is_a: MOD:00670 ! N-acylated residue [Term] id: MOD:00409 name: N-formylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue amino group with a formamido group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NFoRes" EXACT PSI-MOD-short [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 O 1" xref: DiffMono: "27.994915" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00493 ! formylated residue is_a: MOD:00670 ! N-acylated residue [Term] id: MOD:00414 name: monomethylated L-arginine namespace: PSI-MOD def: "A protein modification that effectively replaces one hydrogen atom of an L-arginine residue with one methyl group." [DeltaMass:215] comment: From DeltaMass: formula incorrect, N and O reversed subset: PSI-MOD_slim synonym: "Me1Arg" EXACT PSI-MOD-short [] synonym: "N-methyl Arginyl" EXACT DeltaMass-label [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 14 N 4 O 1" xref: MassAvg: "170.21" xref: MassMono: "170.116761" xref: Origin: "R" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00658 ! methylated arginine [Term] id: MOD:00416 name: phosphorylation of an hydroxyl amino acid with prompt loss of phosphate namespace: PSI-MOD def: "A change resulting in an alteration of the measured molecular mass of a peptide or protein hydroxyl amino acid phosphorylated promptly followed by secondary loss of a neutral trihydrogen phosphate molecular fragment." [UniMod:23] comment: O4-phosphotyrosine does not lose phosphate by this mechanism. subset: PSI-MOD_slim synonym: "Dehydrated" RELATED UniMod-interim [] synonym: "Dehydration" RELATED UniMod-description [] xref: DiffAvg: "-18.02" xref: DiffFormula: "H -2 O -1" xref: DiffMono: "-18.010565" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00432 ! modified residue with neutral loss of phosphate is_a: MOD:00704 ! dehydrated residue [Term] id: MOD:00420 name: 2-pyrrolidone-5-carboxylic acid (Glu) namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to 2-pyrrolidone-5-carboxylic acid." [DeltaMass:16, PubMed:10214721, PubMed:1836357, PubMed:3473473, PubMed:8382902, UniMod:27] comment: From DeltaMass: References: The conversion of glutamic acid to pyroglutamic was reported for the beta-amiloid protein. Miller et.al. Arch. Biochem. Biophy. (1993) 301, 41-52 [DeltaMass]. This is an artifact of treatment with strong acid under anhydrous conditions [JSG]. subset: PSI-MOD_slim synonym: "(S)-5-oxo-2-pyrrolidinecarboxylic acid" EXACT RESID-systematic [] synonym: "Glu->pyro-Glu" RELATED PSI-MS-label [] synonym: "PyrGlu(Glu)" EXACT PSI-MOD-short [] synonym: "Pyro-glu from E" RELATED UniMod-description [] synonym: "pyroglutamic acid" EXACT RESID-alternate [] synonym: "Pyroglutamic Acid formed from Glutamic Acid" EXACT DeltaMass-label [] synonym: "Pyrrolidone carboxylic acid (Glu)" EXACT UniProt-feature [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 5 H 6 N 1 O 2" xref: MassAvg: "112.11" xref: MassMono: "112.039853" xref: Origin: "E" xref: Source: "artifact" xref: TermSpec: "N-term" is_a: MOD:00906 ! modified L-glutamic acid residue is_a: MOD:01048 ! 2-pyrrolidone-5-carboxylic acid [Term] id: MOD:00421 name: C-glycosylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydrogen atom on a carbon with a carbohydrate-like group through a glycosidic bond." [PubMed:18688235] subset: PSI-MOD_slim synonym: "CGlycoRes" EXACT PSI-MOD-short [] is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00425 name: monohydroxylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces one hydrogen atom with a hydroxyl group." [UniMod:35] subset: PSI-MOD_slim synonym: "Hy1Res" EXACT PSI-MOD-short [] synonym: "Oxidation" RELATED UniMod-interim [] synonym: "Oxidation or Hydroxylation" RELATED UniMod-description [] xref: DiffAvg: "16.00" xref: DiffFormula: "O 1" xref: DiffMono: "15.994915" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "C-term" is_a: MOD:00677 ! hydroxylated residue [Term] id: MOD:00426 name: S-glycosylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces a residue hydrogen atom on a sulfur with a carbohydrate-like group through a glycosidic bond" [PubMed:18688235] subset: PSI-MOD_slim synonym: "SGlycoRes" EXACT PSI-MOD-short [] is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00427 name: methylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a methyl group." [DeltaMass:36] comment: From DeltaMass: Average Mass: 14 Average Mass Change:14 References:Methylation of Asparagine (found in phycobiliproteins) Klotz and Glazer (1987) J. Biol. Chem. 262; 17350-17355 subset: PSI-MOD_slim synonym: "MeRes" EXACT PSI-MOD-short [] synonym: "Methylation (N terminus, N epsilon of Lysine, O of Serine, Threonine or C terminus, N of Asparagine)" EXACT DeltaMass-label [] is_a: MOD:00001 ! alkylated residue [Term] id: MOD:00428 name: dihydroxylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces two hydrogen atoms with two hydroxyl groups." [PubMed:12686488, UniMod:425] subset: PSI-MOD_slim synonym: "dihydroxy" RELATED UniMod-description [] synonym: "Dioxidation" RELATED PSI-MS-label [] synonym: "Hy2Res" EXACT PSI-MOD-short [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2" xref: DiffMono: "31.989829" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00677 ! hydroxylated residue [Term] id: MOD:00429 name: dimethylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces two hydrogen atoms with two methyl group." [DeltaMass:0, PubMed:12964758, PubMed:14570711, UniMod:36] comment: For amino-terminal proline residues, dimethylation can effectively only be accomplished with a protonated imino group. This process accounts only for dimethylation and not protonation. The alternative Me2+Res process accounts for both protonation and dimethylation. From DeltaMass: Average Mass: 28. subset: PSI-MOD_slim synonym: "di-Methylation" RELATED UniMod-description [] synonym: "Dimethyl" RELATED PSI-MS-label [] synonym: "Me2Res" EXACT PSI-MOD-short [] synonym: "N,N dimethylation (of Arginine or Lysine)" EXACT DeltaMass-label [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4" xref: DiffMono: "28.031300" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "N-term" is_a: MOD:00427 ! methylated residue [Term] id: MOD:00430 name: trimethylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces three hydrogen atoms with three methyl group" [PubMed:12590383, PubMed:3145979, PubMed:4304194, PubMed:6778808, PubMed:7093227, PubMed:8453381, UniMod:37] comment: For amino acids residues, trimethylation can effectively only be accomplished with a protonated primary amino group. This process accounts only for trimethylation and not protonation. The alternative Me3+Res process accounts for both protonation and trimethylation. subset: PSI-MOD_slim synonym: "Me3Res" EXACT PSI-MOD-short [] synonym: "tri-Methylation" RELATED UniMod-description [] synonym: "Trimethyl" RELATED PSI-MS-label [] xref: DiffAvg: "42.08" xref: DiffFormula: "C 3 H 6" xref: DiffMono: "42.046950" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00427 ! methylated residue [Term] id: MOD:00431 name: modified residue with a secondary neutral loss namespace: PSI-MOD def: "Covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue with a secondary loss of a neutral molecular fragment." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NLModRes" EXACT PSI-MOD-short [] is_a: MOD:01157 ! protein modification categorized by amino acid modified [Term] id: MOD:00432 name: modified residue with neutral loss of phosphate namespace: PSI-MOD def: "Covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue with a secondary loss of a neutral trihydrogen phosphate molecular fragment." [PubMed:18688235] subset: PSI-MOD_slim synonym: "dPhosModRes" EXACT PSI-MOD-short [] is_a: MOD:00431 ! modified residue with a secondary neutral loss [Term] id: MOD:00433 name: glucosylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces a hydrogen atom with an glucose group through a glycosidic bond" [PubMed:18688235] subset: PSI-MOD_slim synonym: "GlcRes" EXACT PSI-MOD-short [] is_a: MOD:00434 ! hexosylated residue [Term] id: MOD:00434 name: hexosylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom of an amino acid residue or of a modifying group with a hexose sugar group through a glycosidic bond." [DeltaMass:203, PubMed:15279557, UniMod:41] comment: From DeltaMass: Average Mass: 162 Formula:C6 H10 05 Monoisotopic Mass Change:162.053 Average Mass Change:162.143 References:PE Sciex. subset: PSI-MOD_slim synonym: "Hex" EXACT PSI-MOD-short [] synonym: "Hex" RELATED PSI-MS-label [] synonym: "Hexose" RELATED UniMod-description [] synonym: "Hexoses (Fru, Gal, Glc, Man)" EXACT DeltaMass-label [] synonym: "O-Glycosyl-" EXACT DeltaMass-label [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00437 name: farnesylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a farnesyl group." [DeltaMass:0, PubMed:15609361, UniMod:44] comment: From DeltaMass: Average Mass: 204 subset: PSI-MOD_slim synonym: "Farnesyl" RELATED PSI-MS-label [] synonym: "Farnesylation" EXACT DeltaMass-label [] synonym: "Farnesylation" RELATED UniMod-description [] synonym: "FarnRes" EXACT PSI-MOD-short [] xref: DiffAvg: "204.35" xref: DiffFormula: "C 15 H 24" xref: DiffMono: "204.187801" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00703 ! isoprenylated residue [Term] id: MOD:00438 name: myristoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a myristoyl group." [DeltaMass:0, UniMod:45] comment: From DeltaMass: Average Mass: 210 subset: PSI-MOD_slim synonym: "Myristoyl" RELATED PSI-MS-label [] synonym: "Myristoylation" EXACT DeltaMass-label [] synonym: "Myristoylation" RELATED UniMod-description [] synonym: "MyrRes" EXACT PSI-MOD-short [] xref: DiffAvg: "210.36" xref: DiffFormula: "C 14 H 26 O 1" xref: DiffMono: "210.198365" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00649 ! acylated residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00440 name: palmitoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a palmitoyl group." [DeltaMass:0, UniMod:47] comment: From DeltaMass: Average Mass: 238 subset: PSI-MOD_slim synonym: "Palmitoyl" RELATED PSI-MS-label [] synonym: "Palmitoylation" EXACT DeltaMass-label [] synonym: "Palmitoylation" RELATED UniMod-description [] synonym: "PamRes" EXACT PSI-MOD-short [] xref: DiffAvg: "238.41" xref: DiffFormula: "C 16 H 30 O 1" xref: DiffMono: "238.229666" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00649 ! acylated residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00441 name: geranylgeranylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a geranylgeranyl group." [DeltaMass:0, PubMed:15609361, UniMod:48] comment: From DeltaMass: Average Mass: 272 subset: PSI-MOD_slim synonym: "Geranyl-geranyl" RELATED UniMod-description [] synonym: "GeranylGeranyl" RELATED PSI-MS-label [] synonym: "Geranylgeranylation" EXACT DeltaMass-label [] synonym: "GergerRes" EXACT PSI-MOD-short [] xref: DiffAvg: "272.47" xref: DiffFormula: "C 20 H 32" xref: DiffMono: "272.250401" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00703 ! isoprenylated residue [Term] id: MOD:00444 name: N-palmitoyl-S-(sn-1-2,3-dipalmitoyl-glycerol)cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to N-palmitoyl-S-(sn-1-2,3-dipalmitoyl-glycerol)cysteine." [PubMed:10356335, UniMod:51] subset: PSI-MOD_slim synonym: "N-acyl diglyceride cysteine" RELATED UniMod-description [] synonym: "Tripalmitate" RELATED PSI-MS-label [] xref: DiffAvg: "789.30" xref: DiffFormula: "C 51 H 96 O 5" xref: DiffMono: "788.725776" xref: Formula: "C 54 H 101 N 1 O 6 S 1" xref: MassAvg: "892.45" xref: MassMono: "891.734961" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00899 ! N-palmitoyl-S-diacylglycerol-L-cysteine relationship: has_functional_parent MOD:01144 ! S-(sn-1-2,3-dipalmitoylglycerol)-L-cysteine [Term] id: MOD:00447 name: N-glucuronylated residue namespace: PSI-MOD def: "modification from UniMod Post-translational" [DeltaMass:0, PubMed:7398618, UniMod:54] comment: From DeltaMass: Average Mass: 176 subset: PSI-MOD_slim synonym: "Glucuronyl" RELATED PSI-MS-label [] synonym: "N-Glucuronyl (N terminus)" EXACT DeltaMass-label [] synonym: "N-glucuronylation" RELATED UniMod-description [] xref: DiffAvg: "176.12" xref: DiffFormula: "C 6 H 8 O 6" xref: DiffMono: "176.032088" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00764 ! glycoconjugated residue [Term] id: MOD:00448 name: N-acetylaminoglucosylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces a hydrogen atom with an N-acetylaminoglucose group through a glycosidic bond" [PubMed:18688235] subset: PSI-MOD_slim synonym: "GlcNAcRes" EXACT PSI-MOD-short [] is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00466 name: glycosylsphingolipidinositolated residue namespace: PSI-MOD def: "A protein modification that effectively converts a residue to a glycosylsphingolipidinositolethanolamidated." [PubMed:12626404, PubMed:18688235, PubMed:8404891] subset: PSI-MOD_slim synonym: "GSIRes" EXACT PSI-MOD-short [] is_a: MOD:00764 ! glycoconjugated residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00476 name: galactosylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces a hydrogen atom with an galactose group through a glycosidic bond" [PubMed:18688235] subset: PSI-MOD_slim synonym: "GalRes" EXACT PSI-MOD-short [] is_a: MOD:00434 ! hexosylated residue [Term] id: MOD:00493 name: formylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a formyl group." [DeltaMass:0, PubMed:15799070, UniMod:122] comment: From DeltaMass: Average Mass: 28 subset: PSI-MOD_slim synonym: "FoRes" EXACT PSI-MOD-short [] synonym: "Formyl" RELATED PSI-MS-label [] synonym: "Formylation" RELATED UniMod-description [] synonym: "Formylation (CHO)" EXACT DeltaMass-label [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 O 1" xref: DiffMono: "27.994915" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: TermSpec: "none" is_a: MOD:00649 ! acylated residue [Term] id: MOD:00498 name: fluorinated residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a fluorine atom for a hydrogen atom." [PubMed:1093385, UniMod:127] subset: PSI-MOD_slim synonym: "Fluoro" RELATED PSI-MS-label [] synonym: "fluorophenylalanine replacement of phenylalanine" RELATED UniMod-description [] synonym: "Fluorophenylalanyl" EXACT DeltaMass-label [] synonym: "FRes" EXACT PSI-MOD-short [] xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00694 ! halogen containing residue [Term] id: MOD:00502 name: triiodinated residue namespace: PSI-MOD def: "A protein modification that effectively substitutes three iodine atoms of a residue for three hydrogen atoms" [PubMed:15627961, PubMed:2026710, UniMod:131] subset: PSI-MOD_slim synonym: "I3Res" EXACT PSI-MOD-short [] synonym: "tri-Iodination" RELATED UniMod-description [] synonym: "Triiodo" RELATED PSI-MS-label [] xref: DiffAvg: "377.69" xref: DiffFormula: "H -3 I 3" xref: DiffMono: "377.689943" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00755 ! iodinated residue [Term] id: MOD:00563 name: N-acetylaminogalactosylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces a hydrogen atom with an N-acetylaminogalactose group through a glycosidic bond" [PubMed:18688235] subset: PSI-MOD_slim synonym: "GalNAcRes" EXACT PSI-MOD-short [] is_a: MOD:00693 ! glycosylated residue [Term] id: MOD:00595 name: mannosylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces a hydrogen atom with an manose group through a glycosidic bond" [PubMed:18688235] subset: PSI-MOD_slim synonym: "ManRes" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00434 ! hexosylated residue [Term] id: MOD:00599 name: monomethylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces one hydrogen atom with one methyl group." [PubMed:11875433, UniMod:34] subset: PSI-MOD_slim synonym: "Me1Res" EXACT PSI-MOD-short [] synonym: "Methyl" RELATED PSI-MS-label [] synonym: "Methylation" RELATED UniMod-description [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2" xref: DiffMono: "14.015650" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00427 ! methylated residue [Term] id: MOD:00601 name: cyclized residue namespace: PSI-MOD def: "A protein modification that effectively produces an heterocyclic amino acid with a covalent bond between the side chain and either its alpha amino or alpha carboxyl group, possibly breaking the peptide chain." [PubMed:18688235] subset: PSI-MOD_slim synonym: "CycRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00602 name: N-methylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom of a residue amino or imino group with an methyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NMeRes" EXACT PSI-MOD-short [] is_a: MOD:00427 ! methylated residue [Term] id: MOD:00644 name: O-acetylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydroxyl group with an acetoxy group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OAcRes" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 O 1" xref: DiffMono: "42.010565" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00394 ! acetylated residue is_a: MOD:00671 ! O-acylated residue [Term] id: MOD:00645 name: S-acetylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue sulfanyl group with an acetylsulfanyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "SAcRes" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 O 1 S 0" xref: DiffMono: "42.010565" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00394 ! acetylated residue is_a: MOD:00672 ! S-acylated residue [Term] id: MOD:00646 name: acetylated L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to either N-acetyl-L-cysteine or S-acetyl-L-cysteine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "AcCys" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1 S 0" xref: DiffMono: "42.010565" xref: Formula: "C 5 H 7 N 1 O 2 S 1" xref: MassAvg: "145.18" xref: MassMono: "145.019749" xref: Origin: "C" xref: Source: "natural" is_a: MOD:00394 ! acetylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00647 name: acetylated L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to either N-acetyl-L-serine, O-acetyl-L-serine, or N,O-diacetyl-L-serine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "AcSer" EXACT PSI-MOD-short [] xref: Origin: "S" xref: Source: "natural" is_a: MOD:00394 ! acetylated residue is_a: MOD:00916 ! modified L-serine residue [Term] id: MOD:00649 name: acylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with an acyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "AcylRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00650 name: N-myristoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue amino group with a myristoylamino group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NMyrRes" EXACT PSI-MOD-short [] is_a: MOD:00438 ! myristoylated residue is_a: MOD:00670 ! N-acylated residue [Term] id: MOD:00651 name: N-palmitoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue amino group with a palmitoylamino group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NPamRes" EXACT PSI-MOD-short [] is_a: MOD:00440 ! palmitoylated residue is_a: MOD:00670 ! N-acylated residue [Term] id: MOD:00652 name: O-palmitoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydroxyl group with a palmitoyloxy group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OPamRes" EXACT PSI-MOD-short [] is_a: MOD:00440 ! palmitoylated residue is_a: MOD:00671 ! O-acylated residue [Term] id: MOD:00653 name: S-palmitoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue sulfanyl group with an palmitoylsulfanyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "SPamRes" EXACT PSI-MOD-short [] is_a: MOD:00440 ! palmitoylated residue is_a: MOD:00672 ! S-acylated residue [Term] id: MOD:00654 name: S-methylated residue namespace: PSI-MOD def: "a protein modification that effectively replaces a sulfanyl group with a methylsulfanyl group" [PubMed:18688235] subset: PSI-MOD_slim synonym: "SMeRes" EXACT PSI-MOD-short [] is_a: MOD:00427 ! methylated residue [Term] id: MOD:00655 name: S-myristoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue sulfanyl group with an myristoylsulfanyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "SMyrRes" EXACT PSI-MOD-short [] is_a: MOD:00438 ! myristoylated residue is_a: MOD:00672 ! S-acylated residue [Term] id: MOD:00656 name: C-methylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydrocarbyl hydrogen with an methyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "CMeRes" EXACT PSI-MOD-short [] is_a: MOD:00427 ! methylated residue [Term] id: MOD:00657 name: L-glutamic acid 5-methyl ester (Gln) namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamine residue to L-glutamate 5-methyl ester." [PubMed:16888, PubMed:6300110, RESID:AA0072, UniMod:528] subset: PSI-MOD_slim synonym: "deamidated 5-methyl esterified glutamine" EXACT PSI-MOD-alternate [] synonym: "Deamidation followed by a methylation" RELATED UniMod-description [] synonym: "Glutamate methyl ester (Gln)" EXACT UniProt-feature [] synonym: "Methyl+Deamidated" RELATED PSI-MS-label [] synonym: "O5MeGlu(Gln)" EXACT PSI-MOD-short [] xref: DiffAvg: "15.01" xref: DiffFormula: "C 1 H 1 N -1 O 1" xref: DiffMono: "14.999666" xref: Formula: "C 6 H 9 N 1 O 3" xref: MassAvg: "143.14" xref: MassMono: "143.058243" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01453 ! L-glutamic acid 5-methyl ester relationship: has_functional_parent MOD:00659 ! methylated glutamine [Term] id: MOD:00658 name: methylated arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to a methylated arginine, either 5-methylargine, N5-methylarginine, or an omega-N-methylated L-arginine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeArg" EXACT PSI-MOD-short [] xref: Origin: "R" is_a: MOD:00427 ! methylated residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00659 name: methylated glutamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamine residue to a methylated glutamine, either 2-methylated glutamine, N5-metylated glutamine, or methyl esterified deamidated glutamine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeGln" EXACT PSI-MOD-short [] xref: Origin: "Q" is_a: MOD:00427 ! methylated residue is_a: MOD:00907 ! modified L-glutamine residue [Term] id: MOD:00660 name: methylated cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to a methylated cysteine, either S-methylcysteine, or cysteine methyl ester." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeCys" EXACT PSI-MOD-short [] xref: Origin: "C" is_a: MOD:00427 ! methylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00661 name: methylated histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to a methylated histidine, such as pros-methylhistidine, or tele-methylhistidine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeHis" EXACT PSI-MOD-short [] synonym: "Methylhistidine" EXACT UniProt-feature [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 9 N 3 O 1" xref: MassAvg: "151.17" xref: MassMono: "151.074562" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00427 ! methylated residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00662 name: methylated leucine namespace: PSI-MOD def: "A protein modification that effectively converts an L-leucine residue to a methylated leucine, either N-methylleucine, or leucine methyl ester." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeLeu" EXACT PSI-MOD-short [] is_a: MOD:00427 ! methylated residue is_a: MOD:00911 ! modified L-leucine residue [Term] id: MOD:00663 name: methylated lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to a methylated lysine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeLys" EXACT PSI-MOD-short [] is_a: MOD:00427 ! methylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00664 name: stereoisomerized residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue L-enantiomer (stereoisomer) with a D-enantiomer or with a different diastereomeric isomer." [PubMed:18688235] subset: PSI-MOD_slim synonym: "D-Res" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00665 name: methylated alanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to a methylated alanine, such as N-methylalanine, N,N-dimethylalanine, or N,N,N-trimethylalanine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeAla" EXACT PSI-MOD-short [] xref: Origin: "A" is_a: MOD:00427 ! methylated residue is_a: MOD:00901 ! modified L-alanine residue [Term] id: MOD:00666 name: octanoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with an octanoyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OctRes" EXACT PSI-MOD-short [] is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00667 name: decanoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a decanoyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "DecRes" EXACT PSI-MOD-short [] is_a: MOD:00649 ! acylated residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00668 name: O-decanoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydroxyl group with a decanoyloxy group." [UniMod:449] subset: PSI-MOD_slim synonym: "Decanoyl" RELATED PSI-MS-label [] synonym: "lipid" RELATED UniMod-description [] synonym: "ODecRes" EXACT PSI-MOD-short [] xref: DiffAvg: "154.25" xref: DiffFormula: "C 10 H 18 N 0 O 1" xref: DiffMono: "154.135765" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00667 ! decanoylated residue is_a: MOD:00671 ! O-acylated residue [Term] id: MOD:00669 name: O-octanoylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydroxyl group with a octanoyloxy group." [UniMod:426] subset: PSI-MOD_slim synonym: "Octanoyl" RELATED PSI-MS-label [] synonym: "octanoyl" RELATED UniMod-description [] synonym: "OOctRes" EXACT PSI-MOD-short [] xref: DiffAvg: "126.20" xref: DiffFormula: "C 8 H 14 N 0 O 1" xref: DiffMono: "126.104465" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00666 ! octanoylated residue is_a: MOD:00671 ! O-acylated residue [Term] id: MOD:00670 name: N-acylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue amino group with a acylamino group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NAcylRes" EXACT PSI-MOD-short [] is_a: MOD:00649 ! acylated residue [Term] id: MOD:00671 name: O-acylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydroxyl group with a acyloxy group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OAcylRes" EXACT PSI-MOD-short [] is_a: MOD:00649 ! acylated residue [Term] id: MOD:00672 name: S-acylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue sulfanyl group with an acylsulfanyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "SAcylRes" EXACT PSI-MOD-short [] is_a: MOD:00649 ! acylated residue [Term] id: MOD:00673 name: methylated asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to a methylated asparagine, such as N4-methyl-L-asparagine, or N4,N4-dimethyl-L-asparagine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeAsn" EXACT PSI-MOD-short [] xref: Origin: "N" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00427 ! methylated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00674 name: amidated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a carboxyl group with a carboxamido group." [PubMed:18688235] subset: PSI-MOD_slim xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00675 name: oxidized residue namespace: PSI-MOD def: "A protein modification that effectively either removes neutral hydrogen atoms (proton and electron), or adds oxygen atoms to a residue with or without the removal of hydrogen atoms." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OxRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00676 name: oxygenated residue namespace: PSI-MOD def: "A protein modification that effectively adds oxygen atoms to a residue with or without the removal of hydrogen atoms." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OxyRes" EXACT PSI-MOD-short [] is_a: MOD:00675 ! oxidized residue [Term] id: MOD:00677 name: hydroxylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with an hydroxyl group." [DeltaMass:0] comment: From DeltaMass: Average Mass: 16 subset: PSI-MOD_slim synonym: "Hydroxylation (of delta C of Lysine, beta C of Tryptophan, C3 or C4 of Proline, beta C of Aspartate)" EXACT DeltaMass-label [] synonym: "HyRes" EXACT PSI-MOD-short [] is_a: MOD:00676 ! oxygenated residue [Term] id: MOD:00678 name: hydroxylated proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to an hydroxylated L-proline." [PubMed:18688235] subset: PSI-MOD_slim synonym: "HyPro" EXACT PSI-MOD-short [] xref: Origin: "P" is_a: MOD:00677 ! hydroxylated residue is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00679 name: carbon oxygenated residue namespace: PSI-MOD def: "A protein modification that effectively adds oxygen atoms to a carbon atom of a residue and removes hydrogen atoms." [PubMed:18688235] subset: PSI-MOD_slim synonym: "COxyRes" EXACT PSI-MOD-short [] is_a: MOD:00676 ! oxygenated residue [Term] id: MOD:00680 name: sulfur oxygenated residue namespace: PSI-MOD def: "A protein modification that effectively adds oxygen atoms to a sulfur atom of a residue without removing hydrogen atoms." [PubMed:18688235] subset: PSI-MOD_slim synonym: "SOxyRes" EXACT PSI-MOD-short [] is_a: MOD:00676 ! oxygenated residue [Term] id: MOD:00681 name: hydroxylated lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to a hydroxylated L-lysine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "HyLys" EXACT PSI-MOD-short [] xref: Origin: "K" is_a: MOD:00677 ! hydroxylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00682 name: hydroxylated arginine namespace: PSI-MOD def: "A protein modification that effectively converts an L-arginine residue to a hydroxylated L-arginine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "HyArg" EXACT PSI-MOD-short [] xref: Origin: "R" is_a: MOD:00677 ! hydroxylated residue is_a: MOD:00902 ! modified L-arginine residue [Term] id: MOD:00683 name: dehydrogenated residue namespace: PSI-MOD def: "A protein modification that effectively removes neutral hydrogen atoms (proton and electron) from a residue." [UniMod:401] subset: PSI-MOD_slim synonym: "dHRes" EXACT PSI-MOD-short [] is_a: MOD:00675 ! oxidized residue [Term] id: MOD:00684 name: deamidated L-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to L-aspartic acid." [PubMed:1097438, PubMed:339692, PubMed:4399050, PubMed:5764436, PubMed:6692818, PubMed:8089117, PubMed:9521123, PubMed:9582379, RESID:AA0004, UniMod:7] comment: incidental to RESID:AA0059 subset: PSI-MOD_slim synonym: "Deamidated asparagine" EXACT UniProt-feature [] synonym: "dNAsn" EXACT PSI-MOD-short [] xref: DiffAvg: "0.98" xref: DiffFormula: "C 0 H -1 N -1 O 1" xref: DiffMono: "0.984016" xref: Formula: "C 4 H 5 N 1 O 3" xref: MassAvg: "115.09" xref: MassMono: "115.026943" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00013 ! L-aspartic acid residue is_a: MOD:00400 ! deamidated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:00685 name: deamidated L-glutamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamine residue to L-glutamic acid." [PubMed:1881881, PubMed:4565668, PubMed:4922541, PubMed:6692818, PubMed:9192900, PubMed:957425, RESID:AA0006, UniMod:7] subset: PSI-MOD_slim synonym: "Deamidated glutamine" EXACT UniProt-feature [] synonym: "dNGln" EXACT PSI-MOD-short [] xref: DiffAvg: "0.98" xref: DiffFormula: "C 0 H -1 N -1 O 1" xref: DiffMono: "0.984016" xref: Formula: "C 5 H 7 N 1 O 3" xref: MassAvg: "129.11" xref: MassMono: "129.042593" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00015 ! L-glutamic acid residue is_a: MOD:00400 ! deamidated residue [Term] id: MOD:00687 name: thioether crosslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two residues by formation of a thioether bond between a cysteine thiol and either an alkyl C as in lanthionine, or an aryl C as 2'-(S-cysteinyl)-L-histidine." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00688 name: isopeptide crosslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two residues with an amide bond where either the donor amino or carboxyl is not an alpha group." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues [Term] id: MOD:00689 name: disulfide crosslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two residues by formation of a disulfide bond with two cysteine thiols." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00690 name: oxazole/thiazole ring crosslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two residues by formation of an oxazole or thiazole ring." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues [Term] id: MOD:00691 name: 5-imidazolinone ring crosslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two residues by formation of an 5-imidazolinone ring." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues [Term] id: MOD:00692 name: uncategorized crosslinked residues namespace: PSI-MOD def: "A protein crosslink modification that is not chemically categorized." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues [Term] id: MOD:00693 name: glycosylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with an carbohydrate-like group through a glycosidic bond." [PubMed:18688235] subset: PSI-MOD_slim synonym: "GlycoRes" EXACT PSI-MOD-short [] xref: Source: "natural" is_a: MOD:00764 ! glycoconjugated residue [Term] id: MOD:00694 name: halogen containing residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a halogen atom for a hydrogen atom." [PubMed:18688235] subset: PSI-MOD_slim synonym: "halogenated residue" EXACT PSI-MOD-alternate [] synonym: "HalRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00695 name: sulfated residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a sulfonyl group for the hydrogen atom of a hydroxyl or sulfanyl group." [DeltaMass:0, PubMed:14752058, UniMod:40] comment: From DeltaMass: Average Mass: 80. subset: PSI-MOD_slim synonym: "O-Sulfonation" RELATED UniMod-description [] synonym: "Sulfo" RELATED PSI-MS-label [] synonym: "SulfRes" EXACT PSI-MOD-short [] synonym: "Sulphonation (SO3H) (of PMC group)" EXACT DeltaMass-label [] xref: DiffAvg: "81.07" xref: DiffFormula: "H 1 O 3 S 1" xref: DiffMono: "80.964640" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00860 ! sulfur containing residue [Term] id: MOD:00696 name: phosphorylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a phosphate group." [DeltaMass:0, UniMod:21] comment: From DeltaMass: Average Mass: 80. subset: PSI-MOD_slim synonym: "Phospho" RELATED PSI-MS-label [] synonym: "Phosphorylation" RELATED UniMod-description [] synonym: "Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine)" EXACT DeltaMass-label [] synonym: "PhosRes" EXACT PSI-MOD-short [] xref: DiffAvg: "79.98" xref: DiffFormula: "H 1 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00861 ! phosphorus containing residue [Term] id: MOD:00697 name: flavin modified residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a flavin group." [UniMod:50] subset: PSI-MOD_slim synonym: "FAD" RELATED PSI-MS-label [] synonym: "Flavin adenine dinucleotide" RELATED UniMod-description [] synonym: "FlavRes" EXACT PSI-MOD-short [] xref: DiffAvg: "783.53" xref: DiffFormula: "C 27 H 31 N 9 O 15 P 2 S 0" xref: DiffMono: "783.141485" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00698 name: metal or metal cluster containing residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a metal atom or a metal cluster for hydrogen atoms, or coordinates a metal ion." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MetalRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00699 name: porphyrin modified residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a porphyrin group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "PorphRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00700 name: tetrapyrrole modified residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a tetrapyrrole group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "TetrapyrRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00701 name: nucleotide or nucleic acid modified residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a nucleotide or a polynucleotide through formation of either a phosphodiester bond, a phosphoramide ester bond, or a glycosidic bond." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NucRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00703 name: isoprenylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a group derived from an isoprene polymer, such as a geranyl (C10), farnesyl (C15) or geranylgeranyl (C20) group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "IpRes" EXACT PSI-MOD-short [] is_a: MOD:00001 ! alkylated residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00704 name: dehydrated residue namespace: PSI-MOD def: "A protein modification that effectively forms a double bond by removing a molecule of water from a residue." [DeltaMass:0, UniMod:23] subset: PSI-MOD_slim synonym: "Dehydrated" RELATED UniMod-interim [] synonym: "Dehydration" RELATED UniMod-description [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00705 name: D-valine namespace: PSI-MOD def: "A protein modification that effectively converts an L-valine residue to D-valine." [ChEBI:30016, PubMed:15853325, RESID:AA0200] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-methylbutanoic acid" EXACT RESID-systematic [] synonym: "alpha-amino-beta-methylbutyric acid" EXACT RESID-alternate [] synonym: "alpha-aminoisovaleric acid" EXACT RESID-alternate [] synonym: "D-Val" EXACT PSI-MOD-short [] synonym: "D-valine" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 5 H 9 N 1 O 1" xref: MassAvg: "99.13" xref: MassMono: "99.068414" xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue [Term] id: MOD:00706 name: dehydrogenated tyrosine namespace: PSI-MOD def: "A protein modification that effectively converts L-tyrosine to 2,3-didehydrotyrosine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "dHTyr" EXACT PSI-MOD-short [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" xref: Formula: "C 9 H 7 N 1 O 2" xref: MassAvg: "161.16" xref: MassMono: "161.047678" xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00683 ! dehydrogenated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00707 name: hydroxylated tyrosine namespace: PSI-MOD def: "a protein modification that effectively converts an L-tyrosine residue to a multihydroxylated L-phenylalanine" [PubMed:18688235] subset: PSI-MOD_slim synonym: "HyTyr" EXACT PSI-MOD-short [] xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00677 ! hydroxylated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00708 name: sulfur oxygenated L-cysteine namespace: PSI-MOD def: "A protein modification that effectively adds oxygen atoms to a sulfur atom of L-cysteine residue without removing hydrogen atoms." [PubMed:18688235] subset: PSI-MOD_slim synonym: "SOxyCys" EXACT PSI-MOD-short [] xref: Origin: "C" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00680 ! sulfur oxygenated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00709 name: sulfur oxygenated L-methionine namespace: PSI-MOD def: "a protein modification that effectively adds oxygen atoms to a sulfur atom of L-methionine" [PubMed:18688235] subset: PSI-MOD_slim synonym: "SOxyMet" EXACT PSI-MOD-short [] xref: Origin: "M" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00680 ! sulfur oxygenated residue is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00710 name: protonated-dimethylated residue namespace: PSI-MOD def: "A protein modification that effectively adds a proton and replaces two hydrogen atoms with two methyl groups." [PubMed:18688235] comment: For N-terminal proline residues, dimethylation can effectively only be accomplished with a protonated imino group. This process accounts for both protonation and dimethylation. The alternative Me2Res process accounts only for dimethylation and not protonation. subset: PSI-MOD_slim synonym: "Me2+Res" EXACT PSI-MOD-short [] is_a: MOD:00429 ! dimethylated residue [Term] id: MOD:00711 name: protonated-trimethylated residue namespace: PSI-MOD def: "A protein modification that effectively adds a proton to an amino group, and replaces three hydrogen atoms with three methyl groups." [PubMed:18688235] comment: For amino acids residues, trimethylation can effectively only be accomplished with a protonated primary amino group. This process accounts for both protonation and trimethylation. The alternative Me3Res process accounts only for trimethylation and not protonation. subset: PSI-MOD_slim synonym: "Me3+Res" EXACT PSI-MOD-short [] is_a: MOD:00427 ! methylated residue [Term] id: MOD:00712 name: methylated proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to a methylated proline, such as N,N-dimethylproline." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MePro" EXACT PSI-MOD-short [] xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00427 ! methylated residue is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00714 name: methylated glycine namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to a methylated glycine, such as N-methylglycine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeGly" EXACT PSI-MOD-short [] xref: Origin: "G" xref: Source: "artifact" xref: TermSpec: "N-term" is_a: MOD:00427 ! methylated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00715 name: methylated isoleucine namespace: PSI-MOD def: "A protein modification that effectively converts an L-isoleucine residue to a methylated isoleucine residue, such as N-methyl-L-isoleucine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeIle" EXACT PSI-MOD-short [] xref: Origin: "I" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00427 ! methylated residue is_a: MOD:00910 ! modified L-isoleucine residue [Term] id: MOD:00716 name: methylated methionine namespace: PSI-MOD def: "A protein modification that effectively converts an L-methionine residue to a methylated methionine, such as N-methyl-L-methionine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeMet" EXACT PSI-MOD-short [] xref: Origin: "M" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00427 ! methylated residue is_a: MOD:00913 ! modified L-methionine residue [Term] id: MOD:00717 name: methylated phenylalanine namespace: PSI-MOD def: "a protein modification that effectively converts an L-phenylalanine residue to a methylated phenylalanine, such as N-methyl-L-phenylalanine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MePhe" EXACT PSI-MOD-short [] xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00427 ! methylated residue is_a: MOD:00914 ! modified L-phenylalanine residue [Term] id: MOD:00718 name: methylated tyrosine namespace: PSI-MOD def: "A protein modification that effectively converts an L-tyrosine residue to a methylated tyrosine, such as N-methyl-L-tyrosine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MeTyr" EXACT PSI-MOD-short [] xref: Origin: "Y" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00427 ! methylated residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00722 name: monomethylated L-glutamine namespace: PSI-MOD def: "a protein modification that effectively replaces one hydrogen atom of an L-glutamine residue with one methyl group" [PubMed:18688235] subset: PSI-MOD_slim synonym: "Me1Gln" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 6 H 10 N 2 O 2" xref: MassAvg: "142.16" xref: MassMono: "142.074228" xref: Origin: "Q" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00659 ! methylated glutamine [Term] id: MOD:00723 name: N-acetylated L-lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to either N2-acetyl-L-lysine, or N6-acetyl-L-lysine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NAcLys" EXACT PSI-MOD-short [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 8 H 15 N 2 O 2" xref: MassAvg: "171.22" xref: MassMono: "171.113353" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00408 ! N-acetylated residue is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:00724 name: N-methylated L-histidine namespace: PSI-MOD def: "A protein modification that effectively replaces one hydrogen atom on a nitrogen of an L-histidine residue with one methyl group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NMeHis" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 7 H 9 N 3 O 1" xref: MassAvg: "151.17" xref: MassMono: "151.074562" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00661 ! methylated histidine [Term] id: MOD:00738 name: iron containing modified residue namespace: PSI-MOD def: "A protein modification that effectively substitutes an iron atom or a cluster containing iron for hydrogen atoms, or that coordinates an iron ion." [PubMed:18688235] subset: PSI-MOD_slim synonym: "FeRes" EXACT PSI-MOD-short [] is_a: MOD:00698 ! metal or metal cluster containing residue [Term] id: MOD:00739 name: iron-sulfur cluster containing modification namespace: PSI-MOD def: "A protein modification that effectively substitutes a cluster of iron and sulfur atoms for hydrogen atoms." [PubMed:18688235] subset: PSI-MOD_slim synonym: "FeSRes" EXACT PSI-MOD-short [] is_a: MOD:00738 ! iron containing modified residue [Term] id: MOD:00740 name: manganese containing modified residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a manganese atom or a cluster containing manganese for hydrogen atoms, or that coordinates a manganese ion." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MnRes" EXACT PSI-MOD-short [] is_a: MOD:00698 ! metal or metal cluster containing residue [Term] id: MOD:00741 name: nickel containing modified residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a nickel atom or a cluster containing nickel for hydrogen atoms, or that coordinates a nickel ion." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NiRes" EXACT PSI-MOD-short [] is_a: MOD:00698 ! metal or metal cluster containing residue [Term] id: MOD:00742 name: copper containing modified residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a copper atom or a cluster containing copper for hydrogen atoms, or that coordinates a copper ion." [PubMed:18688235] subset: PSI-MOD_slim synonym: "CuRes" EXACT PSI-MOD-short [] is_a: MOD:00698 ! metal or metal cluster containing residue [Term] id: MOD:00743 name: molybdenum containing modified residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a molybdenum atom or a cluster containing molybdenum for hydrogen atoms, or that coordinates a molybdenum ion." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MoRes" EXACT PSI-MOD-short [] is_a: MOD:00698 ! metal or metal cluster containing residue [Term] id: MOD:00744 name: molybdenum pterin containing modification namespace: PSI-MOD def: "A protein modification containing a molybdenum atom in a pterin ring system." [PubMed:18688235] subset: PSI-MOD_slim synonym: "MoPterRes" EXACT PSI-MOD-short [] is_a: MOD:00743 ! molybdenum containing modified residue is_a: MOD:00748 ! pterin modified residue [Term] id: MOD:00745 name: selenium containing residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a selenium atom or a cluster containing selenium for hydrogen atoms." [PubMed:18688235] subset: PSI-MOD_slim synonym: "SeRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00748 name: pterin modified residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a pterin group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "PterRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00749 name: sulfur substitution for oxygen namespace: PSI-MOD def: "A protein modification that effectively substitutes a sulfur atom for an oxygen atom." [PubMed:18688235] subset: PSI-MOD_slim synonym: "S(O)Res" EXACT PSI-MOD-short [] is_a: MOD:00860 ! sulfur containing residue [Term] id: MOD:00750 name: deoxyribonucleic acid linked residue namespace: PSI-MOD def: "A protein modification that effectively crosslinks an amino acid residue and the 3'- or 5'-end of DNA through a phosphodiester bond." [PubMed:18688235] subset: PSI-MOD_slim synonym: "DNARes" EXACT PSI-MOD-short [] is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:00751 name: ribonucleic acid linked residue namespace: PSI-MOD def: "a protein modification" [PubMed:18688235] subset: PSI-MOD_slim synonym: "RNARes" EXACT PSI-MOD-short [] is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:00752 name: adenosine diphosphoribosyl (ADP-ribosyl) modified residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with ADP-ribose through formation of a glycosidic bond." [DeltaMass:0] comment: From DeltaMass: Average Mass: 541. subset: PSI-MOD_slim synonym: "ADP-rybosylation (from NAD)" EXACT DeltaMass-label [] synonym: "ADPRRes" EXACT PSI-MOD-short [] is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:00753 name: chlorinated residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a chlorine atom for a hydrogen atom." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ClRes" EXACT PSI-MOD-short [] xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00694 ! halogen containing residue [Term] id: MOD:00754 name: brominated residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a bromine atom for a hydrogen atom." [PubMed:18688235] subset: PSI-MOD_slim synonym: "BrRes" EXACT PSI-MOD-short [] xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00694 ! halogen containing residue [Term] id: MOD:00755 name: iodinated residue namespace: PSI-MOD def: "A protein modification that effectively substitutes an iodine atom of a residue for a hydrogen atom." [PubMed:18688235] subset: PSI-MOD_slim synonym: "IRes" EXACT PSI-MOD-short [] xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00694 ! halogen containing residue [Term] id: MOD:00756 name: 4-hydroxy-D-valine namespace: PSI-MOD def: "A protein modification that effectively converts an L-valine residue to 4-hydroxy-D-valine." [PubMed:15853325, RESID:AA0388] subset: PSI-MOD_slim synonym: "(2R,3Xi)-2-amino-4-hydroxy-3-methylbutanoic acid" EXACT RESID-systematic [] synonym: "D-4-hydroxyvaline" EXACT UniProt-feature [] synonym: "D-4HyVal" EXACT PSI-MOD-short [] synonym: "D-gamma-hydroxyvaline" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 5 H 9 N 1 O 2" xref: MassAvg: "115.13" xref: MassMono: "115.063329" xref: Origin: "V" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00664 ! stereoisomerized residue [Term] id: MOD:00757 name: O4-galactosyl-L-hydroxyproline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to O4-galactosyl-L-hydroxyproline." [RESID:AA0389] comment: secondary to RESID:AA0030 subset: PSI-MOD_slim synonym: "(2S,4R)-4-(beta-D-galactopyranosyloxy)pyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] synonym: "4-(beta-D-galactopyranosyloxy)proline" EXACT RESID-alternate [] synonym: "4-(galactosyloxy)proline" EXACT RESID-alternate [] synonym: "beta-galactopyranosyl-4-hydroxyproline" EXACT RESID-alternate [] synonym: "O4-glycosyl-hydroxyproline" EXACT RESID-alternate [] xref: DiffAvg: "178.14" xref: DiffFormula: "C 6 H 10 N 0 O 6" xref: DiffMono: "178.047738" xref: Formula: "C 11 H 17 N 1 O 7" xref: MassAvg: "275.26" xref: MassMono: "275.100502" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00758 name: O4-(N-acetylamino)glucosyl-L-hydroxyproline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to O4-(N-acetylamino)glucosyl-L-hydroxyproline." [PubMed:15238247, PubMed:9660787, RESID:AA0390] comment: secondary to RESID:AA0030 subset: PSI-MOD_slim synonym: "(2S,4R)-4-[2-acetamido-2-deoxy-alpha-D-glucopyranosyloxy]pyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] synonym: "4-(N-acetylglucosaminyloxy)proline" EXACT RESID-alternate [] synonym: "4-[(2-N-acetylamino)-alpha-D-glucopyranosyl]oxyproline" EXACT RESID-alternate [] synonym: "alpha-2-(N-acetylamino)glucopyranosyl-4-hydroxyproline" EXACT RESID-alternate [] synonym: "O4-glycosyl-hydroxyproline" EXACT RESID-alternate [] xref: DiffAvg: "219.19" xref: DiffFormula: "C 8 H 13 N 1 O 6" xref: DiffMono: "219.074287" xref: Formula: "C 13 H 20 N 2 O 7" xref: MassAvg: "316.31" xref: MassMono: "316.127051" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00915 ! modified L-proline residue [Term] id: MOD:00764 name: glycoconjugated residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a carbohydrate-like group either through formation of a glycosidic bond or through glycation formation of a 1-deoxy-2-keto-1-yl bond." [PubMed:18688235, PubMed:\:3743566] subset: PSI-MOD_slim is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00772 name: vanadium containing modified residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a vanadium atom or a cluster containing vanadium for hydrogen atoms, or that coordinates a vanadium ion." [PubMed:18688235] subset: PSI-MOD_slim synonym: "VRes" EXACT PSI-MOD-short [] is_a: MOD:00698 ! metal or metal cluster containing residue [Term] id: MOD:00783 name: dimethylated L-arginine namespace: PSI-MOD def: "A protein modification that effectively replaces two hydrogen atoms of an L-arginine residue with two methyl groups." [PubMed:18688235] subset: PSI-MOD_slim synonym: "NNMe2Arg" EXACT PSI-MOD-short [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4 N 0 O 0" xref: DiffMono: "28.031300" xref: Formula: "C 8 H 16 N 4 O 1" xref: MassAvg: "184.24" xref: MassMono: "184.132411" xref: Origin: "R" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00429 ! dimethylated residue is_a: MOD:00658 ! methylated arginine [Term] id: MOD:00797 name: 2-(S-L-cysteinyl)pyruvic acid O-phosphothioketal namespace: PSI-MOD def: "a protein modification that effectively converts an L-cysteine residue to the PEP adduct, 2-(S-L-cysteinyl)pyruvic acid O-phosphothioketal" [PubMed:4696757, PubMed:7999765, PubMed:8664284, RESID:AA0391] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[1-carboxy-1-(phosphonooxy)ethyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "cysteinyl pyruvate O-phosphothioketal" EXACT RESID-alternate [] synonym: "Phosphoenolpyruvate (covalent)" EXACT UniProt-feature [] synonym: "phosphoenolpyruvate cysteine adduct" EXACT RESID-alternate [] synonym: "phospholactoyl cysteine adduct" EXACT RESID-alternate [] synonym: "S-[1-carboxy-1-(phosphonooxy)ethyl]cysteine" EXACT RESID-alternate [] synonym: "SPEPCys" EXACT PSI-MOD-short [] xref: DiffAvg: "168.04" xref: DiffFormula: "C 3 H 5 N 0 O 6 P 1 S 0" xref: DiffMono: "167.982375" xref: Formula: "C 6 H 10 N 1 O 7 P 1 S 1" xref: MassAvg: "271.18" xref: MassMono: "270.991559" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00861 ! phosphorus containing residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00799 name: S-galactosyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively forms an S-beta-galactosylated L-cysteine." [PubMed:11945907, RESID:AA0392] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(beta-D-galactopyranosylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "S-(beta-D-galactopyranosyl)cysteine" EXACT RESID-alternate [] synonym: "S-glycosyl-cysteine" EXACT RESID-alternate [] synonym: "SGalCys" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5 S 0" xref: DiffMono: "162.052823" xref: Formula: "C 9 H 15 N 1 O 6 S 1" xref: MassAvg: "265.28" xref: MassMono: "265.062008" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00426 ! S-glycosylated residue is_a: MOD:00476 ! galactosylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00800 name: L-cysteinyl-L-histidino-homocitryl vanadium heptairon nonasulfide namespace: PSI-MOD def: "a protein modification that effectively converts an L-cysteine residue and an L-histidine residue to L-cysteinyl-L-histidino-homocitryl vanadium heptairon nonasulfide" [PubMed:2345152, RESID:AA0393] comment: Cross-link 2; incidental to RESID:AA0300. subset: PSI-MOD_slim synonym: "CysHis-[V7Fe9S]" EXACT PSI-MOD-short [] synonym: "nitrogenase iron-vanadium cofactor" EXACT RESID-alternate [] xref: DiffAvg: "932.56" xref: DiffFormula: "C 7 Fe 7 H 6 N 0 O 7 S 9 V 1" xref: DiffMono: "932.248513" xref: Formula: "C 16 Fe 7 H 18 N 4 O 9 S 10 V 1" xref: MassAvg: "1172.84" xref: MassMono: "1172.316610" xref: Origin: "C, H" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00772 ! vanadium containing modified residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00801 name: L-cysteinyl-L-histidino-homocitryl octairon nonasulfide namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue and an L-histidine residue to L-cysteinyl-L-histidino-homocitryl octairon nonasulfide." [PubMed:8392330, RESID:AA0394] comment: Cross-link 2; incidental to RESID:AA0300. subset: PSI-MOD_slim synonym: "CysHis-[8Fe9S]" EXACT PSI-MOD-short [] synonym: "nitrogenase iron-iron cofactor" EXACT RESID-alternate [] xref: DiffAvg: "937.46" xref: DiffFormula: "C 7 Fe 8 H 6 N 0 O 7 S 9" xref: DiffMono: "937.239491" xref: Formula: "C 16 Fe 8 H 18 N 4 O 9 S 10" xref: MassAvg: "1177.75" xref: MassMono: "1177.307588" xref: Origin: "C, H" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00802 name: L-histidino vanadium tetraoxide namespace: PSI-MOD def: "a protein modification that effectively converts an L-histidine residue to L-histidino vanadium tetraoxide" [PubMed:10543953, PubMed:16494433, PubMed:8552646, RESID:AA0395] subset: PSI-MOD_slim synonym: "(4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-1-yl) (dihydroxy)dioxovanadium" EXACT RESID-alternate [] synonym: "1'-vanadato-L-histidine" EXACT RESID-alternate [] synonym: "bromoperoxidase vanadium cofactor" EXACT RESID-alternate [] synonym: "chloroperoxidase vanadium cofactor" EXACT RESID-alternate [] synonym: "dihydrogen (4-[(2S)-2-amino-2-carboxyethyl]-1H-imidazol-1-yl) (tetraoxido)vanadate" EXACT RESID-systematic [] synonym: "haloperoxidase vanadium cofactor" EXACT RESID-alternate [] synonym: "histidine-1-vanadate" EXACT RESID-alternate [] synonym: "histidine-N(epsilon)-vanadate" EXACT RESID-alternate [] synonym: "histidine-N1'-vanadate" EXACT RESID-alternate [] synonym: "NtauH2VO4His" EXACT PSI-MOD-short [] synonym: "tau-vanadatohistidine" EXACT RESID-alternate [] synonym: "tele-vanadatohistidine" EXACT RESID-alternate [] xref: DiffAvg: "116.95" xref: DiffFormula: "C 0 H 2 N 0 O 4 V 1" xref: DiffMono: "116.939268" xref: Formula: "C 6 H 9 N 3 O 5 V 1" xref: MassAvg: "254.09" xref: MassMono: "253.998180" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00772 ! vanadium containing modified residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00803 name: 3-(S-L-cysteinyl)-L-tyrosine namespace: PSI-MOD def: "A protein modification that effectively cross-links an L-cysteine residue and an L-tyrosine residue by a thioether bond to form 3-(S-L-cysteinyl)-L-tyrosine." [PubMed:15342250, RESID:AA0396] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(S,R)-2-amino-3-(2-amino-2-carboxyethylsulfanyl)-3-(4-hydroxyphenyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(2-amino-2-carboxyethylthio)-3-(4-hydroxyphenyl)propanoic acid" EXACT RESID-alternate [] synonym: "3-(S-cysteinyl)-tyrosine (Cys-Tyr)" EXACT UniProt-feature [] synonym: "S-(3-tyrosinyl)cysteine" EXACT RESID-alternate [] synonym: "XLNKSCys3Tyr" EXACT PSI-MOD-short [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0 S 0" xref: DiffMono: "-2.015650" xref: Formula: "C 12 H 12 N 2 O 3 S 1" xref: MassAvg: "264.30" xref: MassMono: "264.056863" xref: Origin: "C, Y" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00804 name: O-glucosyl-L-serine namespace: PSI-MOD def: "a protein modification that effectively forms a O3-beta-glucosylated L-serine" [PubMed:10734111, PubMed:2105311, PubMed:2511201, RESID:AA0397] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(beta-D-glucopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "O-glycosylserine" EXACT RESID-alternate [] synonym: "O3-glucosylserine" EXACT RESID-alternate [] synonym: "OGlcSer" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 9 H 15 N 1 O 7" xref: MassAvg: "249.22" xref: MassMono: "249.084852" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine is_a: MOD:00433 ! glucosylated residue [Term] id: MOD:00805 name: O-(N-acetylaminoglucosyl)-L-serine namespace: PSI-MOD def: "a protein modification that effectively forms a O3-(N-acetylaminoglucosyl)serine" [PubMed:8404891, RESID:AA0398] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "O-(2-acetylamino-2-deoxy-beta-D-glucopyranosyl)-L-serine" EXACT RESID-alternate [] synonym: "O-(N-acetylglucosaminyl)serine" EXACT RESID-alternate [] synonym: "O-glycosylserine" EXACT RESID-alternate [] synonym: "O-linked (GlcNAc)" EXACT UniProt-feature [] synonym: "O-seryl-beta-N-acetylglucosaminide" EXACT RESID-alternate [] synonym: "O3-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-serine" EXACT RESID-alternate [] synonym: "O3-(N-acetylglucosaminyl)serine" EXACT RESID-alternate [] synonym: "OGlcNAcSer" EXACT PSI-MOD-short [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" xref: Formula: "C 11 H 18 N 2 O 7" xref: MassAvg: "290.27" xref: MassMono: "290.111401" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine is_a: MOD:00448 ! N-acetylaminoglucosylated residue [Term] id: MOD:00806 name: O-(N-acetylaminoglucosyl)-L-threonine namespace: PSI-MOD def: "a protein modification that effectively forms a O3-(N-acetylaminoglucosyl)threonine" [PubMed:8404891, RESID:AA0399] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-(alpha-D-2-acetamido-2-deoxyglucopyranosyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "O-(N-acetylglucosaminyl)-L-threonine" EXACT RESID-alternate [] synonym: "O-glycosylthreonine" EXACT RESID-alternate [] synonym: "O-linked (GlcNAc)" EXACT UniProt-feature [] synonym: "O3-(N-acetylglucosaminyl)threonine" EXACT RESID-alternate [] synonym: "OGlcNAcThr" EXACT PSI-MOD-short [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" xref: Formula: "C 12 H 20 N 2 O 7" xref: MassAvg: "304.30" xref: MassMono: "304.127051" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00005 ! O-glycosyl-L-threonine is_a: MOD:00448 ! N-acetylaminoglucosylated residue [Term] id: MOD:00807 name: pyruvic acid (Ser) namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to pyruvic acid." [DeltaMass:23, PubMed:10085076, PubMed:3042771, PubMed:8464063, RESID:AA0127, UniMod:385] comment: DeltaMass gives mass 70 and difference mass -16 with no formula subset: PSI-MOD_slim synonym: "Pyruvate" EXACT DeltaMass-label [] synonym: "Pyruvic acid (Ser)" EXACT UniProt-feature [] synonym: "Pyruvoyl- (Serine)" EXACT DeltaMass-label [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" xref: DiffMono: "-17.026549" xref: Formula: "C 3 H 3 O 2" xref: MassAvg: "71.05" xref: MassMono: "71.013304" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01154 ! pyruvic acid is_a: MOD:01160 ! deaminated residue [Term] id: MOD:00808 name: O-galactosyl-L-serine namespace: PSI-MOD def: "a protein modification that effectively forms a O3-galactosylserine" [PubMed:666730, RESID:AA0400] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(alpha-D-galactopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "O-glycosylserine" EXACT RESID-alternate [] synonym: "O-linked (Gal)" EXACT UniProt-feature [] synonym: "O3-galactosylserine" EXACT RESID-alternate [] synonym: "OGalSer" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 9 H 15 N 1 O 7" xref: MassAvg: "249.22" xref: MassMono: "249.084852" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine is_a: MOD:00476 ! galactosylated residue [Term] id: MOD:00809 name: O-galactosyl-L-threonine namespace: PSI-MOD def: "a protein modification that effectively forms a O3-galactosylthreonine" [PubMed:2673008, RESID:AA0401] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-(alpha-D-galactopyranosyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "O-glycosylthreonine" EXACT RESID-alternate [] synonym: "O-linked (Gal)" EXACT UniProt-feature [] synonym: "O3-galactosylthreonine" EXACT RESID-alternate [] synonym: "OGalThr" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 10 H 17 N 1 O 7" xref: MassAvg: "263.24" xref: MassMono: "263.100502" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00005 ! O-glycosyl-L-threonine is_a: MOD:00476 ! galactosylated residue [Term] id: MOD:00810 name: O-mannosyl-L-serine namespace: PSI-MOD def: "a protein modification that effectively forms a O3-mannosylserine" [PubMed:391559, RESID:AA0402] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(alpha-D-mannopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "O-glycosylserine" EXACT RESID-alternate [] synonym: "O-linked (Man)" EXACT UniProt-feature [] synonym: "O-mannopyranosylserine" EXACT RESID-alternate [] synonym: "O3-mannosylserine" EXACT RESID-alternate [] synonym: "OManSer" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 9 H 15 N 1 O 7" xref: MassAvg: "249.22" xref: MassMono: "249.084852" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine is_a: MOD:00595 ! mannosylated residue [Term] id: MOD:00811 name: O-mannosyl-L-threonine namespace: PSI-MOD def: "a protein modification that effectively forms a O3-mannosylthreonine" [PubMed:391559, RESID:AA0403] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-(alpha-D-mannopyranosyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "O-glycosylthreonine" EXACT RESID-alternate [] synonym: "O-linked (Man)" EXACT UniProt-feature [] synonym: "O3-mannosylthreonine" EXACT RESID-alternate [] synonym: "OManThr" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 10 H 17 N 1 O 7" xref: MassAvg: "263.24" xref: MassMono: "263.100502" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00005 ! O-glycosyl-L-threonine is_a: MOD:00595 ! mannosylated residue [Term] id: MOD:00812 name: O-fucosyl-L-serine namespace: PSI-MOD def: "A protein modification that effectively converts an serine residue to an O-fucosylserine." [PubMed:10734111, PubMed:11067851, PubMed:11344537, PubMed:12096136, PubMed:1517205, PubMed:15189151, PubMed:1904059, PubMed:3311742, PubMed:3578767, RESID:AA0404, UniMod:295] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(alpha-6-deoxy-D-galactopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "dHex" RELATED PSI-MS-label [] synonym: "Fucose" RELATED UniMod-description [] synonym: "O-glycosylserine" EXACT RESID-alternate [] synonym: "O3-fucosylserine" EXACT RESID-alternate [] synonym: "OFucSer" EXACT PSI-MOD-short [] xref: DiffAvg: "146.14" xref: DiffFormula: "C 6 H 10 N 0 O 4" xref: DiffMono: "146.057909" xref: Formula: "C 9 H 15 N 1 O 6" xref: MassAvg: "233.22" xref: MassMono: "233.089937" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] id: MOD:00813 name: O-fucosyl-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an threonine residue to an O-fucosylthreonine." [PubMed:11344537, PubMed:11857757, PubMed:15189151, PubMed:1740125, PubMed:1900431, RESID:AA0405, UniMod:295] subset: PSI-MOD_slim synonym: "(2S,3R)-2-amino-3-(alpha-6-deoxy-D-galactopyranosyloxy)butanoic acid" EXACT RESID-systematic [] synonym: "dHex" RELATED PSI-MS-label [] synonym: "Fucose" RELATED UniMod-description [] synonym: "O-glycosylthreonine" EXACT RESID-alternate [] synonym: "O-linked (Fuc)" EXACT UniProt-feature [] synonym: "O3-fucosylthreonine" EXACT RESID-alternate [] synonym: "OFucThr" EXACT PSI-MOD-short [] xref: DiffAvg: "146.14" xref: DiffFormula: "C 6 H 10 N 0 O 4" xref: DiffMono: "146.057909" xref: Formula: "C 10 H 17 N 1 O 6" xref: MassAvg: "247.25" xref: MassMono: "247.105587" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00005 ! O-glycosyl-L-threonine [Term] id: MOD:00814 name: O-xylosyl-L-serine namespace: PSI-MOD def: "a protein modification that effectively forms a O3-xylosylserine" [PubMed:8747463, RESID:AA0406] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(alpha-D-xylopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "O-(beta-D-xylopyranosyl)-L-serine" EXACT RESID-alternate [] synonym: "O-glycosylserine" EXACT RESID-alternate [] synonym: "O3-xylosylserine" EXACT RESID-alternate [] synonym: "OXylSer" EXACT PSI-MOD-short [] xref: DiffAvg: "132.11" xref: DiffFormula: "C 5 H 8 N 0 O 4" xref: DiffMono: "132.042259" xref: Formula: "C 8 H 13 N 1 O 6" xref: MassAvg: "219.19" xref: MassMono: "219.074287" xref: Origin: "S" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] id: MOD:00816 name: S-stearoyl-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-stearoyl-L-cysteine." [DeltaMass:0, PubMed:2371783, PubMed:3143715, PubMed:8761467, RESID:AA0407] comment: From DeltaMass: Average Mass: 266 subset: PSI-MOD_slim synonym: "(R)-2-amino-3-(octadecanoylsulfanyl)propanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-(octadecanoylthio)propanoic acid" EXACT RESID-alternate [] synonym: "cysteine octadecanoate thioester" EXACT RESID-alternate [] synonym: "cysteine stearate thioester" EXACT RESID-alternate [] synonym: "S-stearoyl cysteine" EXACT UniProt-feature [] synonym: "SSteCys" EXACT PSI-MOD-short [] synonym: "Stearoylation" EXACT DeltaMass-label [] xref: DiffAvg: "266.46" xref: DiffFormula: "C 18 H 34 N 0 O 1 S 0" xref: DiffMono: "266.260966" xref: Formula: "C 21 H 39 N 1 O 2 S 1" xref: MassAvg: "369.60" xref: MassMono: "369.270150" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00672 ! S-acylated residue is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00817 name: 3'-geranyl-2',3'-dihydro-2',N2-cyclo-L-tryptophan namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to 3'-geranyl-2',3'-dihydro-2',N2-cyclo-L-tryptophan." [ChEBI:35304, PubMed:16407988, PubMed:8168130, RESID:AA0408] subset: PSI-MOD_slim synonym: "(2S,3aR,8aS)-3a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-1,2,3,3a,8,8a-hexahydropyrrolo[2,3-b]indole-2-carboxylic acid" EXACT RESID-systematic [] synonym: "3'-geranyl-2',N2-cyclotryptophan" EXACT UniProt-feature [] synonym: "3'Ger2'N2cycTrp" EXACT PSI-MOD-short [] xref: DiffAvg: "136.23" xref: DiffFormula: "C 10 H 16 N 0 O 0" xref: DiffMono: "136.125201" xref: Formula: "C 21 H 26 N 2 O 1" xref: MassAvg: "322.44" xref: MassMono: "322.204513" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00601 ! cyclized residue [Term] id: MOD:00818 name: glycosylphosphatidylinositolated residue namespace: PSI-MOD def: "A protein modification that effectively converts a residue to a glycosylphosphatidylinositolethanolamidated." [PubMed:12643538, UniMod:394] subset: PSI-MOD_slim synonym: "glycosylphosphatidylinositol" RELATED UniMod-description [] synonym: "GPI-anchor amidated carboxyl end" EXACT UniProt-feature [] synonym: "GPIanchor" RELATED UniMod-interim [] synonym: "GPIRes" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00764 ! glycoconjugated residue is_a: MOD:00861 ! phosphorus containing residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:00819 name: L-2-aminobutanoic acid (Glu) namespace: PSI-MOD def: "A protein modification that effectively converts an L-glutamic acid residue to L-2-aminobutanoic acid." [ChEBI:35619, DeltaMass:0, PubMed:11740505, RESID:AA0409] subset: PSI-MOD_slim synonym: "(S)-2-aminobutanoic acid" EXACT RESID-systematic [] synonym: "Abu" EXACT DeltaMass-label [] synonym: "dCbxGlu" EXACT PSI-MOD-short [] synonym: "L-2-amino-n-butyric acid" EXACT RESID-alternate [] synonym: "L-2-aminobutyric acid" EXACT RESID-alternate [] synonym: "L-alpha-amino-n-butyric acid" EXACT RESID-alternate [] synonym: "L-alpha-aminobutyric acid" EXACT RESID-alternate [] synonym: "L-butyrine" EXACT RESID-alternate [] xref: DiffAvg: "-44.01" xref: DiffFormula: "C -1 H 0 N 0 O -2" xref: DiffMono: "-43.989829" xref: Formula: "C 4 H 7 N 1 O 1" xref: MassAvg: "85.10" xref: MassMono: "85.052764" xref: Origin: "E" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00906 ! modified L-glutamic acid residue [Term] id: MOD:00820 name: 2-imino-alanine 5-imidazolinone glycine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-aspartic acid residue and a glycine residue to form 2-imino-alanine 5-imidazolinone glycine." [PubMed:16627946, RESID:AA0410] comment: Cross-link 2; carboxamidine. subset: PSI-MOD_slim synonym: "2,N-didehydroalanyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "2-(1-iminoethyl)-1-carboxymethyl-1-imidazolin-5-one" EXACT RESID-systematic [] synonym: "2-imino-alanyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "[2-(1-iminoethyl)-5-oxo-4,5-dihydro-imidazol-1-yl]-acetic acid" EXACT RESID-alternate [] synonym: "alanyl-5-imidazolinone glycine" EXACT RESID-alternate [] synonym: "para-hydroxybenzylidene-imidazolidinone chromophore" EXACT RESID-alternate [] synonym: "red fluorescent protein zRFP574 chromophore" EXACT RESID-alternate [] xref: DiffAvg: "-64.04" xref: DiffFormula: "C -1 H -4 N 0 O -3" xref: DiffMono: "-64.016044" xref: Formula: "C 5 H 4 N 2 O 1" xref: MassAvg: "108.10" xref: MassMono: "108.032363" xref: Origin: "D, G" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00691 ! 5-imidazolinone ring crosslinked residues is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:00821 name: S-(L-alanyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-alanine residue and an L-cysteine residue by a thioester bond to form S-(L-alanyl)-L-cysteine." [PubMed:11807079, RESID:AA0411] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2-amino-1-oxopropyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "alanine cysteine thioester" EXACT RESID-alternate [] synonym: "S-(2-aminopropanoyl)cysteine" EXACT RESID-alternate [] synonym: "XLNK1AlaSCys" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 6 H 9 N 2 O 2 S 1" xref: MassAvg: "173.21" xref: MassMono: "173.038474" xref: Origin: "A, C" xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00901 ! modified L-alanine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00822 name: S-(L-leucyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-leucine residue and an L-cysteine residue by a thioester bond to form S-(L-leucyl)-L-cysteine." [PubMed:12591958, RESID:AA0412] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2-amino-4-methyl-1-oxopentyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "leucine cysteine thioester" EXACT RESID-alternate [] synonym: "S-(2-amino-4-methylpentanoyl)cysteine" EXACT RESID-alternate [] synonym: "XLNK1LeuSCys" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 9 H 15 N 2 O 2 S 1" xref: MassAvg: "215.29" xref: MassMono: "215.085424" xref: Origin: "C, L" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00911 ! modified L-leucine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00823 name: S-(L-methionyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-methionine residue and an L-cysteine residue by a thioester bond to form S-(L-methionyl)-L-cysteine." [PubMed:12146974, RESID:AA0413] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2-amino-4-methylsulfanyl-1-oxobutyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "methionine cysteine thioester" EXACT RESID-alternate [] synonym: "S-(2-amino-4-methylthiobutanoyl)cysteine" EXACT RESID-alternate [] synonym: "XLNK1MetSCys" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 8 H 13 N 2 O 2 S 2" xref: MassAvg: "233.33" xref: MassMono: "233.041845" xref: Origin: "C, M" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00913 ! modified L-methionine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00825 name: S-(L-phenylalanyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-phenylalanine residue and an L-cysteine residue by a thioester bond to form S-(L-phenylalaninyl)-L-cysteine." [PubMed:12591958, RESID:AA0414] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2-amino-3-phenyl-1-oxopropyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "phenylalanine cysteine thioester" EXACT RESID-alternate [] synonym: "S-(2-amino-3-phenylpropanoyl)cysteine" EXACT RESID-alternate [] synonym: "XLNK1PheSCys" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 12 H 13 N 2 O 2 S 1" xref: MassAvg: "249.31" xref: MassMono: "249.069774" xref: Origin: "C, F" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00914 ! modified L-phenylalanine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00826 name: S-(L-threonyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-threonine residue and an L-cysteine residue by a thioester bond to form S-(L-threonyl)-L-cysteine." [PubMed:15268951, RESID:AA0415] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(2S,3R)-2-amino-3-hydroxy-1-oxobutyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "S-(2-amino-3-hydroxybutanoyl)cysteine" EXACT RESID-alternate [] synonym: "threonine cysteine thioester" EXACT RESID-alternate [] synonym: "XLNK1ThrSCys" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 7 H 11 N 2 O 3 S 1" xref: MassAvg: "203.24" xref: MassMono: "203.049038" xref: Origin: "C, T" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00827 name: S-(L-tyrosyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-tyrosine residue and an L-cysteine residue by a thioester bond to form S-(L-tyrosyl)-L-cysteine." [PubMed:11807079, RESID:AA0416] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2-amino-3-(4-hydoxyphenyl)-1-oxopropyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "S-[2-amino-3-(4-hydoxyphenyl)propanoyl]cysteine" EXACT RESID-alternate [] synonym: "tyrosine cysteine thioester" EXACT RESID-alternate [] synonym: "XLNK1TyrSCys" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 12 H 13 N 2 O 3 S 1" xref: MassAvg: "265.31" xref: MassMono: "265.064688" xref: Origin: "C, Y" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00919 ! modified L-tyrosine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00828 name: S-(L-tryptophanyl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-tryptophan residue and an L-cysteine residue by a thioester bond to form S-(L-tryptophanyl)-L-cysteine." [PubMed:16030216, RESID:AA0417] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2-amino-3-(1H-indol-3-yl)-1-oxopropyl]sulfanylpropanoic acid" EXACT RESID-systematic [] synonym: "S-[2-amino-3-(1H-indol-3-yl)propanoyl]cysteine" EXACT RESID-alternate [] synonym: "tryptophan cysteine thioester" EXACT RESID-alternate [] synonym: "XLNK1TrpSCys" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 14 H 14 N 3 O 2 S 1" xref: MassAvg: "288.34" xref: MassMono: "288.080673" xref: Origin: "C, W" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00395 ! thioester crosslinked residues is_a: MOD:00918 ! modified L-tryptophan residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00829 name: O-(L-phenylalanyl)-L-serine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-phenylalanine residue and an L-serine residue by an ester bond to form S-(L-phenylalaninyl)-L-serine." [PubMed:12591958, RESID:AA0418] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(R)-2-amino-3-[(S)-2-amino-3-phenyl-1-oxopropyl]oxypropanoic acid" EXACT RESID-systematic [] synonym: "O-(2-amino-3-phenylpropanoyl)serine" EXACT RESID-alternate [] synonym: "phenylalanine serine ester" EXACT RESID-alternate [] synonym: "XLNK1PheOSer" EXACT PSI-MOD-short [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1 S 0" xref: DiffMono: "-18.010565" xref: Formula: "C 12 H 13 N 2 O 3" xref: MassAvg: "233.24" xref: MassMono: "233.092617" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00885 ! ester crosslinked residues is_a: MOD:00914 ! modified L-phenylalanine residue is_a: MOD:00916 ! modified L-serine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00830 name: N-methyl-L-proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to an N-methyl-L-proline." [PubMed:3127388, RESID:AA0419] subset: PSI-MOD_slim synonym: "(S)-1-methylpyrrolidine-2-carboxylic acid" EXACT RESID-systematic [] synonym: "1-methylpyrrolidine-2-carboxylic acid" EXACT RESID-alternate [] synonym: "N-methylated L-proline" EXACT PSI-MOD-alternate [] synonym: "N-methylproline" EXACT UniProt-feature [] synonym: "NMePro" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 6 H 10 N 1 O 1" xref: MassAvg: "112.15" xref: MassMono: "112.076239" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:01417 ! monomethylated proline is_a: MOD:01462 ! N-alpha-methylated proline [Term] id: MOD:00832 name: N4-(N-acetylamino)galactosyl-L-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to an N4-(N-acetamino)galactosyl-asparagine." [PubMed:8262914, RESID:AA0420] subset: PSI-MOD_slim synonym: "(S)-2-amino-4-(2-acetamido-2-deoxy-beta-D-galactopyranosyl)amino-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "N4-(2-acetamido-2-deoxy-beta-D-galactopyranosyl)-L-asparagine" EXACT RESID-alternate [] synonym: "N4-(2-acetylamino-2-deoxy-beta-D-galactopyranosyl)-L-asparagine" EXACT RESID-alternate [] synonym: "N4-(N-acetylgalactosaminyl)asparagine" EXACT RESID-alternate [] synonym: "N4-asparagine-beta-N-acetylgalactosaminide" EXACT RESID-alternate [] synonym: "N4-glycosyl-L-asparagine" EXACT RESID-alternate [] synonym: "N4-glycosylasparagine" EXACT RESID-alternate [] synonym: "N4GalNAcAsn" EXACT PSI-MOD-short [] xref: DiffAvg: "203.19" xref: DiffFormula: "C 8 H 13 N 1 O 5" xref: DiffMono: "203.079373" xref: Formula: "C 12 H 19 N 3 O 7" xref: MassAvg: "317.30" xref: MassMono: "317.122300" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00160 ! N4-glycosyl-L-asparagine is_a: MOD:00563 ! N-acetylaminogalactosylated residue [Term] id: MOD:00833 name: N4-glucosyl-L-asparagine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to an N4-glucosyl-asparagine." [PubMed:1569073, PubMed:3410849, RESID:AA0421] subset: PSI-MOD_slim synonym: "(S)-2-amino-4-(D-glucopyranosyl)amino-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "N4-(D-glucopyranosyl)-L-asparagine" EXACT RESID-alternate [] synonym: "N4-asparagine-glucoside" EXACT RESID-alternate [] synonym: "N4-glucosylasparagine" EXACT RESID-alternate [] synonym: "N4-glycosyl-L-asparagine" EXACT RESID-alternate [] synonym: "N4-glycosylasparagine" EXACT RESID-alternate [] synonym: "N4GlcAsn" EXACT PSI-MOD-short [] xref: DiffAvg: "162.14" xref: DiffFormula: "C 6 H 10 N 0 O 5" xref: DiffMono: "162.052823" xref: Formula: "C 10 H 16 N 2 O 7" xref: MassAvg: "276.24" xref: MassMono: "276.095751" xref: Origin: "N" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00433 ! glucosylated residue [Term] id: MOD:00834 name: O-(N-acetylamino)fucosyl-L-serine namespace: PSI-MOD def: "a protein modification that effectively forms an O3-(N-acetamino)fucosylserine" [PubMed:11342554, PubMed:12010970, RESID:AA0422] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(2-acetamido-2-deoxy-beta-D-fucopyranosyloxy)propanoic acid" EXACT RESID-systematic [] synonym: "O-(2-acetylamino-2-deoxy-beta-D-fucopyranosyl)-L-serine" EXACT RESID-alternate [] synonym: "O-(N-acetylfucosaminyl)serine" EXACT RESID-alternate [] synonym: "O-seryl-beta-N-acetylfucosaminide" EXACT RESID-alternate [] synonym: "O3-(2-acetamido-2-deoxy-beta-D-fucopyranosyl)-L-serine" EXACT RESID-alternate [] synonym: "O3-(N-acetylfucosaminyl)serine" EXACT RESID-alternate [] synonym: "OFucNAcSer" EXACT PSI-MOD-short [] xref: DiffAvg: "187.19" xref: DiffFormula: "C 8 H 13 N 1 O 4" xref: DiffMono: "187.084458" xref: Formula: "C 11 H 18 N 2 O 6" xref: MassAvg: "274.27" xref: MassMono: "274.116486" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00002 ! O-glycosyl-L-serine [Term] id: MOD:00835 name: L-3-oxoalanine (Ser) namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to L-oxoalanine." [DeltaMass:349, PubMed:14563551, PubMed:7628016, PubMed:8681943, PubMed:9276974, PubMed:9478923, RESID:AA0185, UniMod:401] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-oxopropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-oxopropionic acid" EXACT RESID-alternate [] synonym: "3-oxoalanine (Ser)" EXACT UniProt-feature [] synonym: "C(alpha)-formylglycine" RELATED RESID-misnomer [] synonym: "dehydrogenated serine residue" RELATED UniMod-description [] synonym: "Didehydro" RELATED PSI-MS-label [] synonym: "formylglycine" RELATED UniMod-alternate [] synonym: "formylglycine (from serine)" EXACT DeltaMass-label [] synonym: "L-amino-malonic acid semialdehyde" EXACT RESID-alternate [] synonym: "L-aminomalonaldehydic acid" EXACT RESID-alternate [] synonym: "L-serinesemialdehyde" RELATED RESID-misnomer [] synonym: "oxoalanine" RELATED UniMod-alternate [] xref: DiffAvg: "-2.02" xref: DiffFormula: "C 0 H -2 N 0 O 0" xref: DiffMono: "-2.015650" xref: Formula: "C 3 H 3 N 1 O 2" xref: MassAvg: "85.06" xref: MassMono: "85.016378" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00683 ! dehydrogenated residue is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01169 ! L-3-oxoalanine [Term] id: MOD:00848 name: reagent derivatized residue namespace: PSI-MOD def: "A protein modification that is produced by formation of an adduct with a particular compound used as a reagent." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00858 name: D-alanine (Ser) namespace: PSI-MOD def: "A protein modification that effectively converts an L-serine residue to D-alanine." [PubMed:7961627, RESID:AA0191] subset: PSI-MOD_slim synonym: "D-Ala(Ser)" EXACT PSI-MOD-short [] synonym: "D-alanine (Ser)" EXACT UniProt-feature [] xref: DiffAvg: "-16.00" xref: DiffFormula: "C 0 H 0 N 0 O -1" xref: DiffMono: "-15.994915" xref: Formula: "C 3 H 5 N 1 O 1" xref: MassAvg: "71.08" xref: MassMono: "71.037114" xref: Origin: "S" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00862 ! D-alanine is_a: MOD:00916 ! modified L-serine residue is_a: MOD:01161 ! deoxygenated residue [Term] id: MOD:00859 name: modified residue that can arise from different natural residues namespace: PSI-MOD def: "A protein modification that can be derived from different natural residues by different chemical processes." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:01157 ! protein modification categorized by amino acid modified [Term] id: MOD:00860 name: sulfur containing residue namespace: PSI-MOD def: "A protein modification that produces an amino acid residue containing a sulfur atom." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00861 name: phosphorus containing residue namespace: PSI-MOD def: "A protein modification that produces an amino acid residue containing a phosphorus atom." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:00862 name: D-alanine namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to D-alanine." [ChEBI:29949, PubMed:7287302, PubMed:7961627, RESID:AA0191] subset: PSI-MOD_slim synonym: "(R)-2-aminopropanoic acid" EXACT RESID-systematic [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "C 3 H 5 N 1 O 1" xref: MassAvg: "71.08" xref: MassMono: "71.037114" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00859 ! modified residue that can arise from different natural residues [Term] id: MOD:00863 name: D-allo-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to D-allo-threonine." [ChEBI:32826, PubMed:18025465, PubMed:6893271, RESID:AA0199] subset: PSI-MOD_slim synonym: "(2R,3R)-2-amino-3-hydroxybutanoic acid" EXACT RESID-systematic [] synonym: "D-allo-threonine" EXACT RESID-alternate [] synonym: "D-Thr" EXACT PSI-MOD-short [] synonym: "D-threonine" EXACT UniProt-feature [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 4 H 7 N 1 O 2" xref: MassAvg: "101.10" xref: MassMono: "101.047678" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:00864 name: tris-L-cysteinyl L-histidino diiron disulfide namespace: PSI-MOD def: "A protein modification that effectively converts three L-cysteine residues and an L-histidine residue to tris-L-cysteinyl L-histidino diiron disulfide." [PubMed:17766439, PubMed:17766440, RESID:AA0438] comment: Cross-link 4. subset: PSI-MOD_slim synonym: "CDGSH domain iron-sulfur cluster" EXACT RESID-alternate [] synonym: "di-mu-sulfido(bis-S-cysteinyliron)(S-cysteinyl-N3'-histidinoiron)" EXACT RESID-systematic [] xref: DiffAvg: "171.79" xref: DiffFormula: "C 0 Fe 2 H -4 N 0 O 0 S 2" xref: DiffMono: "171.782717" xref: Formula: "C 15 Fe 2 H 18 N 6 O 4 S 5" xref: MassAvg: "618.36" xref: MassMono: "617.869183" xref: Origin: "C, C, C, H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00739 ! iron-sulfur cluster containing modification is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00865 name: N-aspartyl-glycosylsphingolipidinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to N-aspartyl-glycosylsphingolipidinositolethanolamine." [RESID:AA0439] subset: PSI-MOD_slim synonym: "GPI-like-anchor amidated aspartate" EXACT UniProt-feature [] synonym: "GSIAsp" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 6 H 12 N 2 O 7 P 1" xref: MassAvg: "255.14" xref: MassMono: "255.038212" xref: Origin: "D" xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00866 name: dihydroxylated proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to one of several dihydroxylated proline residues, such as (2S,3R,4R)-3,4-dihydroxyproline or (2S,3R,4S)-3,4-dihydroxyproline." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Hy2Pro" EXACT PSI-MOD-short [] xref: DiffAvg: "32.00" xref: DiffFormula: "C 0 H 0 N 0 O 2" xref: DiffMono: "31.989829" xref: Formula: "C 5 H 7 N 1 O 3" xref: MassAvg: "129.11" xref: MassMono: "129.042593" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00428 ! dihydroxylated residue is_a: MOD:00678 ! hydroxylated proline [Term] id: MOD:00868 name: natural, non-standard encoded residue namespace: PSI-MOD def: "A protein modification that inserts or replaces a residue with a natural, non-standard encoded residue, such as N-formyl-L-methionine, L-selenocysteine, or L-pyrrolysine." [PubMed:18688235] comment: These are produced exclusively by modification of amino acids acylated to special tRNA before incorporation by ribosomes into proteins. For this reason, they have also been referred to as pre-translational modifications. subset: PSI-MOD_slim xref: Origin: "X" xref: Source: "natural" is_a: MOD:00009 ! natural residue [Term] id: MOD:00869 name: L-alanine residue (Asp) namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to L-alanine." [PubMed:17138938, RESID:AA0001] comment: This has been reported to occur by a natural process of beta-decarboxylation. subset: PSI-MOD_slim synonym: "Asp(Ala)" EXACT PSI-MOD-short [] synonym: "Beta-decarboxylated aspartate" EXACT UniProt-feature [] xref: DiffAvg: "-44.01" xref: DiffFormula: "C -1 H 0 N 0 O -2" xref: DiffMono: "-43.989829" xref: Formula: "C 3 H 5 N 1 O 1" xref: MassAvg: "71.08" xref: MassMono: "71.037114" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00010 ! L-alanine residue is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:00883 name: alpha-amidated residue namespace: PSI-MOD def: "A protein modification that effectively replaces an alpha-carboxyl group with a carboxamido group." [DeltaMass:0, UniMod:2] subset: PSI-MOD_slim synonym: "Amidated" RELATED PSI-MS-label [] synonym: "Amidation" RELATED UniMod-description [] synonym: "Amide formation (C terminus)" EXACT DeltaMass-label [] synonym: "ResN" EXACT PSI-MOD-short [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00674 ! amidated residue [Term] id: MOD:00885 name: ester crosslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two residues by formation of an ester bond." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues [Term] id: MOD:00886 name: L-6'-chlorotryptophan namespace: PSI-MOD def: "A protein modification that effectively converts an L-tryptophan residue to L-6'-chlorotryptophan." [PubMed:9033387, RESID:AA0180, UniMod:340] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-(6-chloro-1H-indol-3-yl)propanoic acid" EXACT RESID-systematic [] synonym: "6'-chlorotryptophan" EXACT UniProt-feature [] synonym: "6'-ClTrp" EXACT PSI-MOD-short [] xref: DiffAvg: "34.45" xref: DiffFormula: "C 0 Cl 1 H -1 N 0 O 0" xref: DiffMono: "33.961028" xref: Formula: "C 11 Cl 1 H 9 N 2 O 1" xref: MassAvg: "220.65" xref: MassMono: "220.040341" xref: Origin: "W" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00753 ! chlorinated residue is_a: MOD:00918 ! modified L-tryptophan residue [Term] id: MOD:00890 name: phosphorylated L-histidine namespace: PSI-MOD def: "A protein modification that effectively converts an L-histidine residue to a phosphorylated L-histidine, such as pros-phosphohistidine, or tele-phosphohistidine." [PubMed:18688235] subset: PSI-MOD_slim xref: DiffAvg: "79.98" xref: DiffFormula: "C 0 H 1 N 0 O 3 P 1" xref: DiffMono: "79.966331" xref: Formula: "C 6 H 8 N 3 O 4 P 1" xref: MassAvg: "217.12" xref: MassMono: "217.025242" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:00891 name: D-serine namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to D-serine." [ChEBI:29998, PubMed:6893271, PubMed:7973665, RESID:AA0195] subset: PSI-MOD_slim synonym: "(R)-2-amino-3-hydroxypropanoic acid" EXACT RESID-systematic [] synonym: "D-Ser" EXACT PSI-MOD-short [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "C 3 H 5 N 1 O 2" xref: MassAvg: "87.08" xref: MassMono: "87.032028" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00664 ! stereoisomerized residue is_a: MOD:00859 ! modified residue that can arise from different natural residues [Term] id: MOD:00892 name: D-serine (Cys) namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to D-serine." [PubMed:18025465, PubMed:6893271, RESID:AA0195] subset: PSI-MOD_slim synonym: "D-serine (Cys)" EXACT UniProt-feature [] xref: DiffAvg: "-16.07" xref: DiffFormula: "C 0 H 0 N 0 O 1 S -1" xref: DiffMono: "-15.977156" xref: Formula: "C 3 H 5 N 1 O 2" xref: MassAvg: "87.08" xref: MassMono: "87.032028" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00891 ! D-serine is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:00895 name: FAD modified residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a flavin adenine dinucleotide (FAD) group." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00697 ! flavin modified residue is_a: MOD:00861 ! phosphorus containing residue [Term] id: MOD:00896 name: FMN modified residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a riboflavin phosphate (flavin mononucleotide, FMN) group." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00697 ! flavin modified residue is_a: MOD:00861 ! phosphorus containing residue [Term] id: MOD:00899 name: N-palmitoyl-S-diacylglycerol-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to N-palmitoyl-S-diacylglycerol-L-cysteine." [PubMed:18688235] subset: PSI-MOD_slim xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "N-term" relationship: has_functional_parent MOD:00069 ! N-palmitoyl-L-cysteine relationship: has_functional_parent MOD:00116 ! S-diacylglycerol-L-cysteine [Term] id: MOD:00901 name: modified L-alanine residue namespace: PSI-MOD def: "A protein modification that modifies an L-alanine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Alanine derivative" EXACT UniProt-feature [] synonym: "ModAla" EXACT PSI-MOD-short [] xref: Origin: "A" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00010 ! L-alanine residue [Term] id: MOD:00902 name: modified L-arginine residue namespace: PSI-MOD def: "A protein modification that modifies an L-arginine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Arginine derivative" EXACT UniProt-feature [] synonym: "ModArg" EXACT PSI-MOD-short [] xref: Origin: "R" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00011 ! L-arginine residue [Term] id: MOD:00903 name: modified L-asparagine residue namespace: PSI-MOD def: "A protein modification that modifies an L-asparagine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModAsn" EXACT PSI-MOD-short [] xref: Origin: "N" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00012 ! L-asparagine residue [Term] id: MOD:00904 name: modified L-aspartic acid residue namespace: PSI-MOD def: "A protein modification that modifies an L-aspartic acid residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModAsp" EXACT PSI-MOD-short [] xref: Origin: "D" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00013 ! L-aspartic acid residue [Term] id: MOD:00905 name: modified L-cysteine residue namespace: PSI-MOD def: "A protein modification that modifies an L-cysteine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Cysteine derivative" EXACT UniProt-feature [] synonym: "ModCys" EXACT PSI-MOD-short [] xref: Origin: "C" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00014 ! L-cysteine residue [Term] id: MOD:00906 name: modified L-glutamic acid residue namespace: PSI-MOD def: "A protein modification that modifies an L-glutamic acid residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModGlu" EXACT PSI-MOD-short [] xref: Origin: "E" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00015 ! L-glutamic acid residue [Term] id: MOD:00907 name: modified L-glutamine residue namespace: PSI-MOD def: "A protein modification that modifies an L-glutamine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Glutamine derivative" EXACT UniProt-feature [] synonym: "ModGln" EXACT PSI-MOD-short [] xref: Origin: "Q" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00016 ! L-glutamine residue [Term] id: MOD:00908 name: modified glycine residue namespace: PSI-MOD def: "A protein modification that modifies a glycine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModGly" EXACT PSI-MOD-short [] xref: Origin: "G" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00017 ! glycine residue [Term] id: MOD:00909 name: modified L-histidine residue namespace: PSI-MOD def: "A protein modification that modifies an L-histidine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModHis" EXACT PSI-MOD-short [] xref: Origin: "H" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00018 ! L-histidine residue [Term] id: MOD:00910 name: modified L-isoleucine residue namespace: PSI-MOD def: "A protein modification that modifies an L-isoleucine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Isoleucine derivative" EXACT UniProt-feature [] synonym: "ModIle" EXACT PSI-MOD-short [] xref: Origin: "I" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00019 ! L-isoleucine residue [Term] id: MOD:00911 name: modified L-leucine residue namespace: PSI-MOD def: "A protein modification that modifies an L-leucine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModLeu" EXACT PSI-MOD-short [] xref: Origin: "L" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00020 ! L-leucine residue [Term] id: MOD:00912 name: modified L-lysine residue namespace: PSI-MOD def: "A protein modification that modifies an L-lysine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Lysine derivative" EXACT UniProt-feature [] synonym: "ModLys" EXACT PSI-MOD-short [] xref: Origin: "K" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00021 ! L-lysine residue [Term] id: MOD:00913 name: modified L-methionine residue namespace: PSI-MOD def: "A protein modification that modifies an L-methionine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Methionine derivative" EXACT UniProt-feature [] synonym: "ModMet" EXACT PSI-MOD-short [] xref: Origin: "M" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00022 ! L-methionine residue [Term] id: MOD:00914 name: modified L-phenylalanine residue namespace: PSI-MOD def: "A protein modification that modifies an L-phenylalanine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModPhe" EXACT PSI-MOD-short [] xref: Origin: "F" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00023 ! L-phenylalanine residue [Term] id: MOD:00915 name: modified L-proline residue namespace: PSI-MOD def: "A protein modification that modifies an L-proline residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModPro" EXACT PSI-MOD-short [] xref: Origin: "P" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00024 ! L-proline residue [Term] id: MOD:00916 name: modified L-serine residue namespace: PSI-MOD def: "A protein modification that modifies an L-serine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModSer" EXACT PSI-MOD-short [] xref: Origin: "S" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00025 ! L-serine residue [Term] id: MOD:00917 name: modified L-threonine residue namespace: PSI-MOD def: "A protein modification that modifies an L-threonine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModThr" EXACT PSI-MOD-short [] xref: Origin: "T" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00026 ! L-threonine residue [Term] id: MOD:00918 name: modified L-tryptophan residue namespace: PSI-MOD def: "A protein modification that modifies an L-tryptophan residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModTrp" EXACT PSI-MOD-short [] synonym: "Tryptophan derivative" EXACT UniProt-feature [] xref: Origin: "W" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00027 ! L-tryptophan residue [Term] id: MOD:00919 name: modified L-tyrosine residue namespace: PSI-MOD def: "A protein modification that modifies an L-tyrosine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModTyr" EXACT PSI-MOD-short [] xref: Origin: "Y" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00028 ! L-tyrosine residue [Term] id: MOD:00920 name: modified L-valine residue namespace: PSI-MOD def: "A protein modification that modifies an L-valine residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ModVal" EXACT PSI-MOD-short [] xref: Origin: "V" is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00029 ! L-valine residue [Term] id: MOD:00924 name: N6-(L-threonyl)-L-lysine namespace: PSI-MOD def: "A protein modification that effectively crosslinks an L-lysine residue and an L-threonine residue by an isopeptide bond to form N6-(L-threonyl)-L-lysine." [PubMed:18063774, RESID:AA0440] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2S)-2-amino-6-([(2S,3R)-2-amino-3-hydroxybutanoyl]amino)hexanoic acid" EXACT RESID-systematic [] synonym: "N6-threonyl-lysine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 10 H 18 N 3 O 3" xref: MassAvg: "228.27" xref: MassMono: "228.134816" xref: Origin: "K, T" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00688 ! isopeptide crosslinked residues is_a: MOD:00912 ! modified L-lysine residue is_a: MOD:00917 ! modified L-threonine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00946 name: crosslinked residues with loss of ammonia namespace: PSI-MOD def: "A protein modification that crosslinks two residues with a covalent bond and the loss of ammonia." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues [Term] id: MOD:00952 name: (2-aminosuccinimidyl)acetic acid namespace: PSI-MOD def: "A protein modification that crosslinks an aspartic acid and the following glycine residue with the formation of (2-aminosuccinimidyl)acetic acid." [PubMed:10801322, RESID:AA0441] comment: Cross-link 2; this cross-link is formed by the condensation of an aspartic acid residue with the alpha-amido of the following residue. subset: PSI-MOD_slim synonym: "(3-amino-2,5-dioxopyrrolidin-1-yl)acetic acid" EXACT RESID-alternate [] synonym: "[(3S)-3-amino-2,5-dioxopyrrolidin-1-yl]acetic acid" EXACT RESID-systematic [] synonym: "N-(2-aminosuccinyl)glycine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 6 H 6 N 2 O 3" xref: MassAvg: "154.12" xref: MassMono: "154.037842" xref: Origin: "D, G" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00904 ! modified L-aspartic acid residue is_a: MOD:00908 ! modified glycine residue is_a: MOD:00954 ! crosslinked residues with loss of water [Term] id: MOD:00954 name: crosslinked residues with loss of water namespace: PSI-MOD def: "A protein modification that crosslinks two residues with a covalent bond and the loss of water." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00033 ! crosslinked residues [Term] id: MOD:00972 name: monobrominated L-phenylalanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-phenylalanine residue to a monobrominated L-phenylalanine, such as L-2'-bromophenylalanine." [PubMed:18688235] comment: From DeltaMass: Average Mass: 78 Average Mass Change:78 References:Yoshino,K et.al. Biochemistry Vol. 30 pg 6203-9 (1991) Identifidation of a novel amino acid, o-bromo-L-phenylananine, in egg-associated peptides that activate spermatozoa subset: PSI-MOD_slim synonym: "Br1Phe" EXACT PSI-MOD-short [] synonym: "bromination" RELATED UniMod-description [] synonym: "Bromo" RELATED PSI-MS-label [] xref: DiffAvg: "78.90" xref: DiffFormula: "Br 1 C 0 H -1 N 0 O 0" xref: DiffMono: "77.910512" xref: Formula: "Br 1 C 9 H 8 N 1 O 1" xref: MassAvg: "226.07" xref: MassMono: "224.978926" xref: Origin: "F" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00754 ! brominated residue [Term] id: MOD:00985 name: halogenated tyrosine namespace: PSI-MOD def: "A protein modification that effectively substitutes a hydrogen atom of an L-tyrosine residue with a halogen atom." [PubMed:18688235] subset: PSI-MOD_slim synonym: "HalTyr" EXACT PSI-MOD-short [] xref: Origin: "Y" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00694 ! halogen containing residue is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:00998 name: iodinated tyrosine namespace: PSI-MOD def: "A protein modification that effectively substitutes a hydrogen atom of an L-tyrosine residue with an iodine atom." [PubMed:18688235] subset: PSI-MOD_slim synonym: "ITyr" EXACT PSI-MOD-short [] xref: Origin: "Y" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00755 ! iodinated residue is_a: MOD:00985 ! halogenated tyrosine [Term] id: MOD:01024 name: monohydroxylated proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to one of several monohydroxylated proline residues, including 3-hydroxy-L-proline and 4-hydroxy-L-proline." [DeltaMass:0] comment: From DeltaMass: Average Mass: 131 subset: PSI-MOD_slim synonym: "Hy1Pro" EXACT PSI-MOD-short [] synonym: "Hydroxyproline" EXACT UniProt-feature [] synonym: "Hydroxyproline" EXACT DeltaMass-label [] synonym: "Hyp" EXACT DeltaMass-label [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 5 H 7 N 1 O 2" xref: MassAvg: "113.11" xref: MassMono: "113.047678" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00678 ! hydroxylated proline [Term] id: MOD:01047 name: monohydroxylated lysine namespace: PSI-MOD def: "A protein modification that effectively converts an L-lysine residue to a monohydroxylated lysine." [DeltaMass:168] comment: From DeltaMass: Average Mass: 144 Abbreviation:-Hyl- Formula:C6H12N2O2 Monoisotopic Mass Change:144.09 Average Mass Change:144.174. subset: PSI-MOD_slim synonym: "Hy1Lys" EXACT PSI-MOD-short [] synonym: "Hydroxy Lysyl (-Hyl-)" EXACT DeltaMass-label [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 6 H 12 N 2 O 2" xref: MassAvg: "144.17" xref: MassMono: "144.089878" xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00681 ! hydroxylated lysine [Term] id: MOD:01048 name: 2-pyrrolidone-5-carboxylic acid namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to 2-pyrrolidone-5-carboxylic acid." [PubMed:18688235] comment: From DeltaMass: Average Mass: -18 Average Mass Change:-18.01 References:The conversion of glutamic acid to pyroglutamic was reported for the beta-amiloid protein.Miller et.al. Arch. Biochem. Biophy. (1993) 301, 41-52. subset: PSI-MOD_slim synonym: "PyrGlu" EXACT PSI-MOD-short [] synonym: "Pyrrolidone carboxylic acid" EXACT RESID-alternate [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "C 5 H 6 N 1 O 2" xref: MassAvg: "112.11" xref: MassMono: "112.039853" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "N-term" is_a: MOD:00601 ! cyclized residue is_a: MOD:00859 ! modified residue that can arise from different natural residues [Term] id: MOD:01110 name: isoprenylated cysteine namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom of an L-cysteine residue with a group derived from an isoprene polymer, such as a geranyl (C10), farnesyl (C15) or geranylgeranyl (C20)." [PubMed:18688235] subset: PSI-MOD_slim synonym: "IpCys" EXACT PSI-MOD-short [] is_a: MOD:00703 ! isoprenylated residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01116 name: S-farnesyl-L-cysteine methyl ester namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-farnesyl-L-cysteine methyl ester." [PubMed:15609361, RESID:AA0102] subset: PSI-MOD_slim synonym: "(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic methyl ester" EXACT RESID-systematic [] synonym: "2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic methyl ester" EXACT RESID-alternate [] synonym: "SFarnOMeCys" EXACT PSI-MOD-short [] xref: DiffAvg: "218.38" xref: DiffFormula: "C 16 H 26 N 0 O 0 S 0" xref: DiffMono: "218.203451" xref: Formula: "C 19 H 32 N 1 O 2 S 1" xref: MassAvg: "338.53" xref: MassMono: "338.215375" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00905 ! modified L-cysteine residue relationship: has_functional_parent MOD:00111 ! S-farnesyl-L-cysteine relationship: has_functional_parent MOD:00114 ! L-cysteine methyl ester [Term] id: MOD:01119 name: S-geranylgeranyl-L-cysteine methyl ester namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-geranylgeranyl-L-cysteine methyl ester." [PubMed:1483450, PubMed:15609361, RESID:AA0104] subset: PSI-MOD_slim synonym: "(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic methyl ester" EXACT RESID-systematic [] synonym: "2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic methyl ester" EXACT RESID-alternate [] synonym: "SGergerOMeCys" EXACT PSI-MOD-short [] xref: DiffAvg: "286.49" xref: DiffFormula: "C 21 H 34 N 0 O 0 S 0" xref: DiffMono: "286.266051" xref: Formula: "C 24 H 40 N 1 O 2 S 1" xref: MassAvg: "406.64" xref: MassMono: "406.277976" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00905 ! modified L-cysteine residue relationship: has_functional_parent MOD:00113 ! S-geranylgeranyl-L-cysteine relationship: has_functional_parent MOD:00114 ! L-cysteine methyl ester [Term] id: MOD:01133 name: S-12-hydroxyfarnesyl-L-cysteine methyl ester namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-12-hydroxyfarnesyl-L-cysteine methyl ester." [PubMed:17790543, RESID:AA0103] subset: PSI-MOD_slim synonym: "(R,E,E,Z)-2-amino-3-(12-hydroxy-3,7,11-trimethyl-3,6,10-dodecatrienylsulfanyl)propanoic methyl ester" EXACT RESID-systematic [] synonym: "2-amino-3-(12-hydroxy-3,7,11-trimethyl-3,6,10-dodecatrienylthio)propanoic methyl ester" EXACT RESID-alternate [] synonym: "S12HyFarnOMeCys" EXACT PSI-MOD-short [] xref: DiffAvg: "234.38" xref: DiffFormula: "C 16 H 26 N 0 O 1 S 0" xref: DiffMono: "234.198365" xref: Formula: "C 19 H 32 N 1 O 3 S 1" xref: MassAvg: "354.53" xref: MassMono: "354.210290" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "C-term" is_a: MOD:00905 ! modified L-cysteine residue relationship: has_functional_parent MOD:00112 ! S-12-hydroxyfarnesyl-L-cysteine relationship: has_functional_parent MOD:00114 ! L-cysteine methyl ester [Term] id: MOD:01144 name: S-(sn-1-2,3-dipalmitoylglycerol)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-(sn-1-2,3-dipalmitoyl-glycerol)cysteine." [DeltaMass:0, PubMed:10896212, PubMed:4575979, PubMed:9056182, RESID:AA0107] comment: From DeltaMass: Average Mass: 524 subset: PSI-MOD_slim synonym: "S-(sn-1-Dipalmitoyl-glyceryl)- (on Cysteine)" EXACT DeltaMass-label [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00116 ! S-diacylglycerol-L-cysteine [Term] id: MOD:01148 name: ubiquitinylated lysine namespace: PSI-MOD def: "A protein modification that effectively crosslinks the N6-amino of a peptidyl lysine with the carboxyl-terminal glycine of a ubiquitin." [PubMed:11125103, PubMed:18688235] subset: PSI-MOD_slim xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00908 ! modified glycine residue is_a: MOD:00912 ! modified L-lysine residue relationship: contains MOD:00134 ! N6-glycyl-L-lysine [Term] id: MOD:01149 name: sumoylated lysine namespace: PSI-MOD def: "A protein modification that effectively crosslinks the N6-amino of a peptidyl lysine with the carboxyl-terminal glycine of a sumo (Small Ubiquitin-related MOdifier) protein." [PubMed:12612601, PubMed:18688235] subset: PSI-MOD_slim xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00908 ! modified glycine residue is_a: MOD:00912 ! modified L-lysine residue relationship: contains MOD:00134 ! N6-glycyl-L-lysine [Term] id: MOD:01150 name: neddylated lysine namespace: PSI-MOD def: "A protein modification that effectively crosslinks the N6-amino of a peptidyl lysine with the carboxyl-terminal glycine of a nedd8 protein." [PubMed:11125103, PubMed:12612601, PubMed:18688235] subset: PSI-MOD_slim xref: Origin: "K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00908 ! modified glycine residue is_a: MOD:00912 ! modified L-lysine residue relationship: contains MOD:00134 ! N6-glycyl-L-lysine [Term] id: MOD:01152 name: carboxylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with a carboxylic acid group." [UniMod:299] subset: PSI-MOD_slim synonym: "Carboxy" RELATED UniMod-interim [] synonym: "Carboxylation" RELATED UniMod-description [] xref: DiffAvg: "44.01" xref: DiffFormula: "C 1 H 0 N 0 O 2" xref: DiffMono: "43.989829" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01153 name: methylthiolated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a hydrogen atom with an sulfanylmethyl group (thiomethyl group)." [UniMod:39] subset: PSI-MOD_slim synonym: "Beta-methylthiolation" RELATED UniMod-description [] synonym: "Methylthio" RELATED UniMod-interim [] xref: DiffAvg: "46.09" xref: DiffFormula: "C 1 H 2 N 0 O 0 S 1" xref: DiffMono: "45.987721" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01154 name: pyruvic acid namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid to pyruvic acid." [PubMed:10085076, PubMed:3042771, PubMed:8464063, RESID:AA0127] subset: PSI-MOD_slim synonym: "2-oxopropanoic acid" EXACT RESID-systematic [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "C 3 H 3 O 2" xref: MassAvg: "71.05" xref: MassMono: "71.013304" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "N-term" is_a: MOD:00859 ! modified residue that can arise from different natural residues [Term] id: MOD:01155 name: lipoconjugated residue namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a lipid-like group either through acylation, alkylation, or amidation." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01156 name: protein modification categorized by chemical process namespace: PSI-MOD def: "Modified amino acid residue derived from a natural amino acid by a real or hypothetical chemical process." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00000 ! protein modification [Term] id: MOD:01157 name: protein modification categorized by amino acid modified namespace: PSI-MOD def: "A protein modification considered either as modified amino acid residues derived from natural amino acids, as a replacement by another natural amino acid, or as a replacement by an unnatural amino acid." [PubMed:18688235] subset: PSI-MOD_slim is_a: MOD:00000 ! protein modification [Term] id: MOD:01158 name: modified L-selenocysteine residue namespace: PSI-MOD def: "A protein modification that modifies an L-selenocysteine residue." [PubMed:18688235] subset: PSI-MOD_slim xref: Origin: "U" is_a: MOD:00745 ! selenium containing residue is_a: MOD:01157 ! protein modification categorized by amino acid modified relationship: derives_from MOD:00031 ! L-selenocysteine residue [Term] id: MOD:01159 name: peptidoglycanated residue namespace: PSI-MOD def: "A protein modification that effectively attaches a residue to murein peptidoglycan by a pentaglycine linker peptide." [PubMed:18688235] subset: PSI-MOD_slim xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00764 ! glycoconjugated residue [Term] id: MOD:01160 name: deaminated residue namespace: PSI-MOD def: "A protein modification that effectively results in the loss of an ammonia, usually by a process of vicinal dehydration, rearrangement, and rehydration with release of ammonia, resulting in a loss of nitrogen with no gain of oxygen." [UniMod:385] subset: PSI-MOD_slim synonym: "Ammonia-loss" RELATED UniMod-interim [] synonym: "Loss of ammonia" RELATED UniMod-description [] xref: DiffAvg: "-17.03" xref: DiffFormula: "C 0 H -3 N -1 O 0" xref: DiffMono: "-17.026549" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01161 name: deoxygenated residue namespace: PSI-MOD def: "A protein modification that effectively removes oxygen atoms from a residue without the removal of hydrogen atoms." [PubMed:14235557, UniMod:447] subset: PSI-MOD_slim synonym: "Deoxy" RELATED PSI-MS-label [] synonym: "dOxyRes" EXACT PSI-MOD-short [] synonym: "reduction" RELATED UniMod-description [] xref: DiffAvg: "-16.00" xref: DiffFormula: "C 0 H 0 N 0 O -1" xref: DiffMono: "-15.994915" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:01472 ! reduced residue [Term] id: MOD:01163 name: guanylated residue namespace: PSI-MOD def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphoguanosine through either a phosphodiester or a phosphoramide bond." [DeltaMass:304, UniMod:413] comment: From DeltaMass: (formula incorrect, N and O reversed) Average Mass: 345 Formula: C10H12O5N7P1 Monoisotopic Mass Change: 345.047 Average Mass Change: 345.209. subset: PSI-MOD_slim synonym: "5'phos Guanosyl" EXACT DeltaMass-label [] synonym: "phospho-guanosine" RELATED UniMod-description [] synonym: "Phosphoguanosine" RELATED PSI-MS-label [] xref: DiffAvg: "345.21" xref: DiffFormula: "C 10 H 12 N 5 O 7 P 1" xref: DiffMono: "345.047434" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:01164 name: riboflavin-phosphoryl namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct with a compound containing a riboflavin phosphate (flavin mononucleotide, FMN) group through a phosphodiester bond." [UniMod:442] subset: PSI-MOD_slim synonym: "FMN" RELATED PSI-MS-label [] synonym: "O3-(riboflavin phosphoryl)" RELATED UniMod-description [] xref: DiffAvg: "438.33" xref: DiffFormula: "C 17 H 19 N 4 O 8 P 1" xref: DiffMono: "438.094050" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00896 ! FMN modified residue [Term] id: MOD:01165 name: adenylated residue namespace: PSI-MOD def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphoadenosine through either a phosphodiester or a phosphoramide bond." [DeltaMass:0, UniMod:405] comment: From DeltaMass: (name misspelled "5'phos adenosinyl") Average Mass: 329 subset: PSI-MOD_slim synonym: "5'phos Adenosinyl" EXACT DeltaMass-label [] synonym: "AMP binding site" RELATED UniMod-description [] synonym: "Phosphoadenosine" RELATED PSI-MS-label [] xref: DiffAvg: "329.21" xref: DiffFormula: "C 10 H 12 N 5 O 6 P 1" xref: DiffMono: "329.052520" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:01166 name: uridylated residue namespace: PSI-MOD def: "A protein modification that effectively crosslinks an amino acid residue and 5'-phosphouridine through either a phosphodiester or a phosphoramide bond." [DeltaMass:292, UniMod:417] comment: From DeltaMass: (name misspelled "5'phos Uridinyl" and formula incorrect, N and O reversed) Average Mass: 306 Formula: C9H11O2N8P1 Monoisotopic Mass Change: 306.025 Average Mass Change: 306.17 subset: PSI-MOD_slim synonym: "5'phos Uridinyl" EXACT DeltaMass-label [] synonym: "PhosphoUridine" RELATED PSI-MS-label [] synonym: "uridine phosphodiester" RELATED UniMod-description [] xref: DiffAvg: "306.17" xref: DiffFormula: "C 9 H 11 N 2 O 8 P 1" xref: DiffMono: "306.025302" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00701 ! nucleotide or nucleic acid modified residue [Term] id: MOD:01167 name: molybdopterin guanine dinucleotide namespace: PSI-MOD def: "modification from UniMod" [UniMod:424] subset: PSI-MOD_slim synonym: "molybdenum bis(molybdopterin guanine dinucleotide)" RELATED UniMod-description [] synonym: "MolybdopterinGD" RELATED PSI-MS-label [] xref: DiffAvg: "1572.03" xref: DiffFormula: "C 40 H 47 Mo 1 N 20 O 26 P 4 S 4" xref: DiffMono: "1572.985775" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "none" is_a: MOD:00744 ! molybdenum pterin containing modification [Term] id: MOD:01168 name: dehydroalanine namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to dehydroalanine." [PubMed:10220322, PubMed:1547888, PubMed:1815586, PubMed:2914619, PubMed:6838602, PubMed:7947813, PubMed:8239649, RESID:AA0181] comment: incidental to RESID:AA0178 subset: PSI-MOD_slim synonym: "2,3-didehydroalanine" EXACT RESID-alternate [] synonym: "2-aminopropenoic acid" EXACT RESID-systematic [] synonym: "4-methylidene-imidazole-5-one active site" EXACT RESID-alternate [] synonym: "anhydroserine" EXACT RESID-alternate [] synonym: "dHAla" EXACT PSI-MOD-short [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "C 3 H 3 N 1 O 1" xref: MassAvg: "69.06" xref: MassMono: "69.021464" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues [Term] id: MOD:01169 name: L-3-oxoalanine namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-oxoalanine." [DeltaMass:349, PubMed:14563551, PubMed:7628016, PubMed:8681943, PubMed:9478923, RESID:AA0185] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-oxopropanoic acid" EXACT RESID-systematic [] synonym: "2-amino-3-oxopropionic acid" EXACT RESID-alternate [] synonym: "C(alpha)-formylglycine [misnomer]" RELATED RESID-misnomer [] synonym: "L-amino-malonic acid semialdehyde" EXACT RESID-alternate [] synonym: "L-aminomalonaldehydic acid" EXACT RESID-alternate [] synonym: "L-serinesemialdehyde [misnomer]" RELATED RESID-misnomer [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "C 3 H 3 N 1 O 2" xref: MassAvg: "85.06" xref: MassMono: "85.016378" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00859 ! modified residue that can arise from different natural residues [Term] id: MOD:01170 name: pyruvic acid iminylated residue namespace: PSI-MOD def: "A protein modification that effectively forms a 2-ketoimine of pyruvicacid with a residue amino group." [UniMod:422] subset: PSI-MOD_slim synonym: "N-pyruvic acid 2-iminyl" RELATED UniMod-description [] synonym: "PyruvicAcidIminyl" RELATED PSI-MS-label [] xref: DiffAvg: "70.05" xref: DiffFormula: "C 3 H 2 N 0 O 2" xref: DiffMono: "70.005479" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "none" xref: TermSpec: "N-term" is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01171 name: O-acetyl-L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to O-acetyl-L-threonine." [PubMed:16728640, RESID:AA0423, UniMod:1] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-acetyloxypropanoic acid" EXACT RESID-systematic [] synonym: "Acetylation" RELATED UniMod-description [] synonym: "O-acetylthreonine" EXACT RESID-alternate [] synonym: "OAcThr" EXACT PSI-MOD-short [] synonym: "threonine acetate ester" EXACT RESID-alternate [] xref: DiffAvg: "42.04" xref: DiffFormula: "C 2 H 2 N 0 O 1" xref: DiffMono: "42.010565" xref: Formula: "C 6 H 9 N 1 O 3" xref: MassAvg: "143.14" xref: MassMono: "143.058243" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00644 ! O-acetylated residue is_a: MOD:01186 ! acetylated L-threonine [Term] id: MOD:01172 name: N-alanyl-glycosylsphingolipidinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to N-alanyl-glycosylsphingolipidinositolethanolamine." [PubMed:12626404, RESID:AA0424] subset: PSI-MOD_slim synonym: "GPI-like-anchor amidated alanine" EXACT UniProt-feature [] synonym: "GSIAla" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 5 H 12 N 2 O 5 P 1" xref: MassAvg: "211.13" xref: MassMono: "211.048383" xref: Origin: "A" xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00901 ! modified L-alanine residue [Term] id: MOD:01173 name: N-asparaginyl-glycosylsphingolipidinositolethanolamine namespace: PSI-MOD def: "A protein modification that effectively converts an L-asparagine residue to N-asparaginyl-glycosylsphingolipidinositolethanolamine." [PubMed:12626404, RESID:AA0425] subset: PSI-MOD_slim synonym: "GPI-like-anchor amidated asparagine" EXACT UniProt-feature [] synonym: "GSIAsn" EXACT PSI-MOD-short [] xref: DiffAvg: "123.05" xref: DiffFormula: "C 2 H 6 N 1 O 3 P 1" xref: DiffMono: "123.008530" xref: Formula: "C 6 H 13 N 3 O 6 P 1" xref: MassAvg: "254.16" xref: MassMono: "254.054197" xref: Origin: "N" xref: Source: "hypothetical" xref: TermSpec: "C-term" is_a: MOD:00466 ! glycosylsphingolipidinositolated residue is_a: MOD:00903 ! modified L-asparagine residue [Term] id: MOD:01174 name: S-(15-deoxy-Delta12,14-prostaglandin J2-9-yl)-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively converts an L-cysteine residue to S-(15-deoxy-Delta12,14-prostaglandin J2-9-yl)-L-cysteine." [ChEBI:27485, PubMed:11466314, PubMed:12684535, RESID:AA0426] subset: PSI-MOD_slim synonym: "(2R)-2-amino-3-([(5Z,9Xi,12E,14Z)-1-hydroxy-1,11-oxoprosta-5,12,14-trien-9-yl]sulfanyl)propanoic acid" EXACT RESID-alternate [] synonym: "(5Z,9Xi,12E,14Z)-9-([(2R)-2-amino-3-carboxyethyl]sulfanyl)-11-oxoprosta-5,12,14-trien-1-oic acid" EXACT RESID-systematic [] synonym: "PG-J2Cys" EXACT PSI-MOD-short [] xref: DiffAvg: "316.43" xref: DiffFormula: "C 20 H 28 N 0 O 3 S 0" xref: DiffMono: "316.203845" xref: Formula: "C 23 H 33 N 1 O 4 S 1" xref: MassAvg: "419.58" xref: MassMono: "419.213030" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00905 ! modified L-cysteine residue is_a: MOD:01155 ! lipoconjugated residue [Term] id: MOD:01175 name: S-phycourobilin-L-cysteine namespace: PSI-MOD def: "A protein modification that effectively results from forming an adduct between a cysteine residue and the tetrapyrrole compound phycourobilin." [PubMed:1903388, PubMed:3208761, PubMed:3838747, RESID:AA0427] subset: PSI-MOD_slim synonym: "(2S,3R,16R)-18-ethenyl-3-[(1R)-1-([(R)-2-amino-2-carboxyethyl]sulfanyl)ethyl]-8,12-bis(2-carboxyethyl)-2,7,13,17-tetramethyl-4,5,15,16-tetrahydrobiline-1,19(21H,22H,24H)-dione" EXACT RESID-systematic [] synonym: "18-ethenyl-3-[1-(2-amino-2-carboxyethylsulfanyl)ethyl]-2,3,15,16-dihydro-2,7,13,17-tetramethyl-1,19-dioxo-(21H,22H,24H)-bilin-8,12-dipropanoic acid" EXACT RESID-alternate [] synonym: "phycourobilin cysteine adduct" EXACT RESID-alternate [] synonym: "PUBCys" EXACT PSI-MOD-short [] xref: DiffAvg: "586.68" xref: DiffFormula: "C 33 H 38 N 4 O 6 S 0" xref: DiffMono: "586.279135" xref: Formula: "C 36 H 43 N 5 O 7 S 1" xref: MassAvg: "689.82" xref: MassMono: "689.288320" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00700 ! tetrapyrrole modified residue is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01176 name: L-dehydrolysinonorleucine namespace: PSI-MOD def: "modification from RESID" [PubMed:16929109, RESID:AA0430] comment: Cross-link 2. subset: PSI-MOD_slim synonym: "(2R)-6-[(5R)-5-amino-5-carboxypentyl]imino-2-aminohexanoic acid" EXACT RESID-systematic [] synonym: "dehydrolysinorleucine [misspelling]" EXACT RESID-alternate [] synonym: "dehydrolysylnorleucine" EXACT RESID-alternate [] synonym: "didehydrolysinonorleucine" EXACT RESID-alternate [] synonym: "L-6,N6-didehydrolysino-L-norleucine" EXACT RESID-alternate [] synonym: "N6-[(S)-5-amino-5-carboxypentylidene]-L-lysine" EXACT RESID-alternate [] synonym: "XLNK6NleN6Lys" EXACT PSI-MOD-short [] xref: DiffAvg: "-19.05" xref: DiffFormula: "C 0 H -5 N -1 O 0" xref: DiffMono: "-19.042199" xref: Formula: "C 12 H 19 N 3 O 2" xref: MassAvg: "237.30" xref: MassMono: "237.147727" xref: Origin: "K, K" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00692 ! uncategorized crosslinked residues is_a: MOD:00912 ! modified L-lysine residue [Term] id: MOD:01177 name: 1'-(1,2,3-trihydroxyprop-2-yl)-L-histidine namespace: PSI-MOD def: "modification from RESID" [PubMed:16760471, RESID:AA0431] subset: PSI-MOD_slim synonym: "(S)-2-amino-3-[1-(1,2,3-trihydroxypropan-2-yl)-1H-imidazol-4-yl]propanoic acid" EXACT RESID-systematic [] synonym: "1-[1,2-dihydroxy-1-(hydroxymethyl)ethyl]-L-histidine" EXACT RESID-alternate [] synonym: "N(epsilon)-histidine dihydroxyacetone adduct" EXACT RESID-alternate [] synonym: "NtauDHAHis" EXACT PSI-MOD-short [] synonym: "tau-(1,2,3-trihydroxypropan-2-yl)histidine" EXACT RESID-alternate [] synonym: "tele-(1,2,3-trihydroxypropan-2-yl)histidine" EXACT RESID-alternate [] xref: DiffAvg: "90.08" xref: DiffFormula: "C 3 H 6 N 0 O 3" xref: DiffMono: "90.031694" xref: Formula: "C 9 H 13 N 3 O 4" xref: MassAvg: "227.22" xref: MassMono: "227.090606" xref: Origin: "H" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00909 ! modified L-histidine residue [Term] id: MOD:01178 name: S-(aspart-4-yloxy) thiocarbonate namespace: PSI-MOD def: "a protein modification that effectively converts an L-aspartic acid residue to S-(aspart-4-yloxy) thiocarbonate" [PubMed:16627948, RESID:AA0432] subset: PSI-MOD_slim synonym: "(2S)-2-amino-4-(carboxysulfanyl)oxy-4-oxobutanoic acid" EXACT RESID-systematic [] synonym: "4-aspartyloxysulfanylcarbonate" EXACT RESID-alternate [] synonym: "AspOSCO2H" EXACT PSI-MOD-short [] synonym: "O-carboxysulfanyl-4-oxo-L-homoserine" EXACT RESID-alternate [] xref: DiffAvg: "76.07" xref: DiffFormula: "C 1 H 0 N 0 O 2 S 1" xref: DiffMono: "75.961900" xref: Formula: "C 5 H 5 N 1 O 5 S 1" xref: MassAvg: "191.16" xref: MassMono: "190.988843" xref: Origin: "D" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:01179 name: N,N-dimethyl-L-alanine namespace: PSI-MOD def: "A protein modification that effectively converts an L-alanine residue to N,N-dimethyl-L-alanine." [PubMed:17691833, PubMed:387091, RESID:AA0433] subset: PSI-MOD_slim synonym: "(S)-1-carboxy-N,N-dimethylaminoethane" EXACT RESID-alternate [] synonym: "(S)-2-(dimethylamino)propanoic acid" EXACT RESID-systematic [] synonym: "N,N-dimethylalanine" EXACT RESID-alternate [] synonym: "NMe2Ala" EXACT PSI-MOD-short [] xref: DiffAvg: "28.05" xref: DiffFormula: "C 2 H 4 N 0 O 0" xref: DiffMono: "28.031300" xref: Formula: "C 5 H 10 N 1 O 1" xref: MassAvg: "100.14" xref: MassMono: "100.076239" xref: Origin: "A" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00429 ! dimethylated residue [Term] id: MOD:01180 name: 2-hydroxyglycine observational artifact namespace: PSI-MOD def: "A protein modification that effectively converts a glycine residue to 2-hydroxyglycine." [ChEBI:38048, PubMed:16178056, PubMed:17431180, PubMed:17823333, RESID:AA0434] comment: CAUTION - peptides of 2-hydroxyglycine are known to be unstable, decaying to break the peptide backbone or to form peptidyl amides [see J. Am. Chem. Soc. 111, 1933-1934, 1989, and J. Org. Chem. 57, 3916-3921, 1992]. If computer analysis of tandem mass-spectrometric results predicts this modification, then it is most probable that there are multiple isobaric peptides differing in the location of multiple hydroxylation modifications [JSG]. subset: PSI-MOD_slim synonym: "2HyGly" EXACT PSI-MOD-short [] synonym: "alpha-hydroxyglycine" EXACT RESID-alternate [] synonym: "amino(hydroxy)acetic acid" EXACT RESID-systematic [] synonym: "aminohydroxyacetic acid" EXACT RESID-alternate [] xref: DiffAvg: "16.00" xref: DiffFormula: "C 0 H 0 N 0 O 1" xref: DiffMono: "15.994915" xref: Formula: "C 2 H 3 N 1 O 2" xref: MassAvg: "73.05" xref: MassMono: "73.016378" xref: Origin: "G" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00425 ! monohydroxylated residue is_a: MOD:00908 ! modified glycine residue [Term] id: MOD:01185 name: 4-amidated L-aspartic acid namespace: PSI-MOD def: "A protein modification that effectively converts an L-aspartic acid residue to L-asparagine." [PubMed:17962566, RESID:AA0003] subset: PSI-MOD_slim synonym: "4NAsp" EXACT PSI-MOD-short [] synonym: "Amidated aspartic acid" EXACT UniProt-feature [] xref: DiffAvg: "-0.98" xref: DiffFormula: "C 0 H 1 N 1 O -1" xref: DiffMono: "-0.984016" xref: Formula: "C 4 H 6 N 2 O 2" xref: MassAvg: "114.10" xref: MassMono: "114.042927" xref: Origin: "D" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00012 ! L-asparagine residue is_a: MOD:00674 ! amidated residue is_a: MOD:00904 ! modified L-aspartic acid residue [Term] id: MOD:01186 name: acetylated L-threonine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to either N-acetyl-L-threonne, or O-acetyl-Lthreonine." [PubMed:18688235] subset: PSI-MOD_slim synonym: "AcThr" EXACT PSI-MOD-short [] xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00394 ! acetylated residue is_a: MOD:00917 ! modified L-threonine residue [Term] id: MOD:01187 name: L-pyrrolysine residue namespace: PSI-MOD def: "A protein modification that inserts or replaces a residue with an L-pyrrolysine residue, a natural pretranslational modification." [ChEBI:21860, PubMed:11435424, PubMed:12029131, PubMed:12029132, PubMed:15314242, PubMed:16096277, RESID:AA0321, UniMod:435] subset: PSI-MOD_slim synonym: "Pyl" EXACT PSI-MOD-short [] xref: DiffAvg: "0.00" xref: DiffFormula: "C 0 H 0 N 0 O 0" xref: DiffMono: "0.000000" xref: Formula: "C 12 H 19 N 3 O 2" xref: MassAvg: "237.30" xref: MassMono: "237.147727" xref: Origin: "O" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00868 ! natural, non-standard encoded residue [Term] id: MOD:01352 name: nitrotyrosine namespace: PSI-MOD def: "modification from UniMod Chemical derivative -" [PubMed:14678012, PubMed:8839040, PubMed:9252331, UniMod:354] comment: One or more isobaric isomers produced by nitration with peroxynitrite reagent. [JSG] subset: PSI-MOD_slim synonym: "Nitrated tyrosine" EXACT UniProt-feature [] synonym: "Nitro" RELATED PSI-MS-label [] synonym: "Oxidation to nitro" RELATED UniMod-description [] xref: DiffAvg: "45.00" xref: DiffFormula: "H -1 N 1 O 2" xref: DiffMono: "44.985078" xref: Formula: "C 9 H 8 N 2 O 4" xref: MassAvg: "208.17" xref: MassMono: "208.048407" xref: Origin: "Y" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00919 ! modified L-tyrosine residue [Term] id: MOD:01417 name: monomethylated proline namespace: PSI-MOD def: "A protein modification that effectively converts an L-proline residue to a monomethylated proline." [PubMed:18688235] subset: PSI-MOD_slim synonym: "Me1Pro" EXACT PSI-MOD-short [] xref: DiffAvg: "14.03" xref: DiffFormula: "C 1 H 2 N 0 O 0" xref: DiffMono: "14.015650" xref: Formula: "C 6 H 10 N 1 O 1" xref: MassAvg: "112.15" xref: MassMono: "112.076239" xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00599 ! monomethylated residue is_a: MOD:00712 ! methylated proline [Term] id: MOD:01420 name: thiazole/thiazoline ring croslinked residues namespace: PSI-MOD def: "A protein modification that crosslinks two residues by condensation of a cysteine thiol with the carbonyl of the preceding residue to form a thiazole or thiazoline ring." [PubMed:18688235] subset: PSI-MOD_slim xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "C" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00687 ! thioether crosslinked residues is_a: MOD:00690 ! oxazole/thiazole ring crosslinked residues is_a: MOD:00905 ! modified L-cysteine residue [Term] id: MOD:01441 name: natural, standard, encoded residue namespace: PSI-MOD def: "A protein modification that inserts or replaces a residue with a natural, standard, encoded residue." [PubMed:18688235, PubMed:6692818] subset: PSI-MOD_slim xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00009 ! natural residue [Term] id: MOD:01453 name: L-glutamic acid 5-methyl ester namespace: PSI-MOD def: "A protein modification that effectively converts a source amino acid residue to L-glutamate 5-methyl ester." [RESID:AA0072] subset: PSI-MOD_slim synonym: "5-methyl esterified L-glutamic acid" EXACT PSI-MOD-alternate [] synonym: "Glutamate methyl ester (Glu)" EXACT UniProt-feature [] synonym: "O-methyl Glutamyl" EXACT DeltaMass-label [] synonym: "O5MeGlu" EXACT PSI-MOD-short [] xref: DiffAvg: "none" xref: DiffFormula: "none" xref: DiffMono: "none" xref: Formula: "C 6 H 9 N 1 O 3" xref: MassAvg: "143.14" xref: MassMono: "143.058243" xref: Origin: "X" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00393 ! O-methylated residue is_a: MOD:00599 ! monomethylated residue is_a: MOD:00859 ! modified residue that can arise from different natural residues [Term] id: MOD:01462 name: N-alpha-methylated proline namespace: PSI-MOD def: "A protein modification that effectively replaces an L-proline alpha imino hydrogen with a methyl group." [PubMed:18688235] subset: PSI-MOD_slim xref: Origin: "P" xref: Source: "natural" xref: TermSpec: "N-term" is_a: MOD:00712 ! methylated proline [Term] id: MOD:01470 name: (E)-dehydrobutyrine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to (E)-dehydrobutyrine." [DeltaMass:0, PubMed:1547888, PubMed:3769923, RESID:AA0182, UniMod:23] subset: PSI-MOD_slim synonym: "(E)-2-amino-butenoic acid" EXACT RESID-systematic [] synonym: "2,3-didehydrobutyrine" EXACT UniProt-feature [] synonym: "2,3-didehydrobutyrine" EXACT RESID-alternate [] synonym: "alpha,beta-dehydroaminobutyric acid" EXACT RESID-alternate [] synonym: "anhydrothreonine" EXACT RESID-alternate [] synonym: "Dehydrated" RELATED UniMod-interim [] synonym: "Dehydration" RELATED UniMod-description [] synonym: "Dehydroamino butyric acid" EXACT DeltaMass-label [] synonym: "dHyThr" EXACT PSI-MOD-short [] synonym: "methyl-dehydroalanine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 4 H 5 N 1 O 1" xref: MassAvg: "83.09" xref: MassMono: "83.037114" xref: Origin: "T" xref: Source: "hypothetical" xref: TermSpec: "none" is_a: MOD:00190 ! dehydrobutyrine [Term] id: MOD:01471 name: (Z)-dehydrobutyrine namespace: PSI-MOD def: "A protein modification that effectively converts an L-threonine residue to (Z)-dehydrobutyrine" [DeltaMass:0, PubMed:1547888, PubMed:3769923, RESID:AA0182, UniMod:23] subset: PSI-MOD_slim synonym: "(Z)-2-amino-butenoic acid" EXACT RESID-systematic [] synonym: "2,3-didehydrobutyrine" EXACT UniProt-feature [] synonym: "2,3-didehydrobutyrine" EXACT RESID-alternate [] synonym: "alpha,beta-dehydroaminobutyric acid" EXACT RESID-alternate [] synonym: "anhydrothreonine" EXACT RESID-alternate [] synonym: "Dehydrated" RELATED UniMod-interim [] synonym: "Dehydration" RELATED UniMod-description [] synonym: "Dehydroamino butyric acid" EXACT DeltaMass-label [] synonym: "dHyThr" EXACT PSI-MOD-short [] synonym: "methyl-dehydroalanine" EXACT RESID-alternate [] xref: DiffAvg: "-18.02" xref: DiffFormula: "C 0 H -2 N 0 O -1" xref: DiffMono: "-18.010565" xref: Formula: "C 4 H 5 N 1 O 1" xref: MassAvg: "83.09" xref: MassMono: "83.037114" xref: Origin: "T" xref: Source: "natural" xref: TermSpec: "none" is_a: MOD:00190 ! dehydrobutyrine [Term] id: MOD:01472 name: reduced residue namespace: PSI-MOD def: "A protein modification that effectively either adds neutral hydrogen atoms (proton and electron), or removes oxygen atoms from a residue with or without the addition of hydrogen atoms." [PubMed:18688235] subset: PSI-MOD_slim synonym: "RedRes" EXACT PSI-MOD-short [] is_a: MOD:01156 ! protein modification categorized by chemical process [Term] id: MOD:01473 name: hydrogenated residue namespace: PSI-MOD def: "A protein modification that effectively adds neutral hydrogen atoms (proton and electron) to a residue." [PubMed:18688235] subset: PSI-MOD_slim synonym: "HRes" EXACT PSI-MOD-short [] is_a: MOD:01472 ! reduced residue [Term] id: MOD:01482 name: calcium containing modified residue namespace: PSI-MOD def: "A protein modification that effectively substitutes a calcium atom or a cluster containing calcium for hydrogen atoms, or that coordinates a calcium ion." [PubMed:18688235] subset: PSI-MOD_slim synonym: "CaRes" EXACT PSI-MOD-short [] is_a: MOD:00698 ! metal or metal cluster containing residue [Term] id: MOD:01483 name: O-formylated residue namespace: PSI-MOD def: "A protein modification that effectively replaces a residue hydroxyl group with a formyloxy group." [PubMed:18688235] subset: PSI-MOD_slim synonym: "OFoRes" EXACT PSI-MOD-short [] xref: DiffAvg: "28.01" xref: DiffFormula: "C 1 O 1" xref: DiffMono: "27.994915" xref: Formula: "none" xref: MassAvg: "none" xref: MassMono: "none" xref: Origin: "X" xref: Source: "artifact" xref: TermSpec: "none" is_a: MOD:00493 ! formylated residue is_a: MOD:00671 ! O-acylated residue [Typedef] id: contains name: contains namespace: PSI-MOD def: "'Entity A' contains 'Entity B' implies that 'Entity B' is a part of the structure of 'Entity A'." [PubMed:18688235] comment: The inverse relationship to "part of". is_transitive: true [Typedef] id: derives_from name: derives from namespace: PSI-MOD def: "'Entity A' derives_from 'Entity B' implies that 'Entity A' is chemically derived from 'Entity B'." [PubMed:18688235] is_transitive: true [Typedef] id: has_functional_parent name: has functional parent namespace: PSI-MOD def: "'Entity A' has_functional_parent 'Entity B' implies that 'Entity B' has at least one chacteristic group from which 'Entity A' can be derived by functional modification." [PubMed:18688235] comment: This relationship indicates that the formula and mass of the child are not inherited from the mass of the parent. is_transitive: true [Typedef] id: part_of name: part of namespace: PSI-MI def: "'Entity A' part_of 'Entity B' implies that 'Entity A' is a part of the structure of 'Entity B'." [PubMed:18688235] is_transitive: true