A brief updates of PSI-MS efforts


  • ASMS meeting (June 8 - 12, 2003) and PSI-MS group plan (Sandra Orchard et al, Functional Genomics, October, 2003) A series of joint ASMS/PSI meetings were held at 51st Annual Conference of the American Society for Mass Spectrometry (ASMS) to further define the scope and essential components of a draft standard for exchanging experimental data from proteomics experiments involving mass spectrometry. A plan was developed to establish a draft proteomics standard for public review. It has been identified that peak lists are one of the minimum data components that would need to be shared between laboratories. Thus, a first draft of the XML-schema describing the peak lists should be developed and released to the public to allow public review. It is hoped that instrument vendors and software developers, such as protein search engine vendors, will test the XML format to represent peak list and experimental metadata and provide feedback to the HUPO-PSI. The second stage of this plan includes adding the remaining proteomics data to the model, including search engine results, sample preparation and separation method information and other data items needed to complete a proteomics data repository record. The meeting notes are here.

  • The 1st draft XML-schema and converting tools: A working group was assembled at the EBI to work on the peak list part of a draft XML-schema (now called mzData) and associated controlled vocabularies, as well as the tools to convert the vendor specific formats to this draft XML format. The working group met from July 21 to July 25 and consisted of Randy Julian (Eli Lilly, USA), Weimin Zhu (EBI), Kai Runte (EBI), Henning Hermjakob (EBI), Chris Taylor (University of Manchester, UK), and Pierre-Alian Binz, Khaled Mostaguir and Roberto Fabbretti from SIB, Switzerland. A discussion about the modification of PEDRo model, leading to MIAPE, a MIAMI-like proteomics data model, to reflect this draft standard was also initiated.

    In the weeks following the EBI meeting, members of this work group will continue to finalize the following deliverables for review by the PSI committee with the goal of presentation at the next HUPO conference:
        a. The 1st draft of the mzData XML-schema describing peak lists and associated metadata (by controlled vocabularies)
        b. Java converting tools to reformat some vendor-specific peak list files into standard XML or Base64 formats;
        c. A possible demo, with some user cases and real sample files.
    Currently, the mzData XML schema is in the PSI sourceforge CVS repository, and further developments will be continuously deposited there. Please send your comments and suggestions to our Sourceforge mailing list.

    Weimin Zhu, July 30th, 2003