Topic outline

  • General

    Proteome X Change Consortium

    Data sharing in proteomics: databases, repositories, standards, data submission

    Lausanne, 20-22 November 2013

    Proteomics, and in particular the use of Mass Spectrometry in Proteomics, does generate large amounts of data. These data are used to derive biologically relevant knowledge. Journals and founders are recommending, if not requesting, that data supporting results are submitted to dedicated repositories such as PRIDE and PASSEL. A portion of these data is used to populate knowledgebases such as UniProtKB and NeXtProt. Mechanisms such as ProteomeXchange exist that help scientists with data deposition, data query and data recovery.

    The course is organized by the SIB Swiss Institute of Bioinformatics (Pierre-Alain Binz) and supported by the ProteomeXchange consortium.

    Coverage of the course

    The course will cover various aspects of the data sharing process:

    Importance of sequences databases and knowledgebases for proteomics
    - How experimental data is used to annotate knowledgebases such as UniProtKB and NeXtProt
    - What from these resources is available for MS-based data analysis (not only fasta files)

      About ProteomeXchange and data standards
      - Description of the ProteomeXchange consortium and submission tool
      - The PRIDE and PASSEL data repositories
      - The use of data standards (HUPO-PSI)
      - Importance of data deposition from a journal editor's point of view

        Selected usecases will also illustrate advantages and limitations of this mechanism
        - Application in proteogenomics
        - Design and validation of a precise quantitation method
        - SWATH and dealing with large datasets
        - Use and qualification of repository data for prediction and data mining

          Target audience

          Proteomics scientists and bioinformaticians interested in understanding existing mechanisms for sharing and publishing their data (in particular Mass Spectrometry derived ones), as well as those interested in understanding how repositories and knowledgebases may make use of and represent these data. Expected are PhD students, post docs and senior scientists.


          • Prior Proteomics and Mass spectrometry knowledge is required to attend the course
          • Participants should bring their own computers (with wi-fi)


          The registration is closed.

          The registration fees for academics are 150 CHF. The fees include course content material, coffee breaks and a social dinner (on the 21st). Participants from non-academic institutions should contact us.

          Potential participants can subscribe to our course announcement mailing-list and will be kept updated with news about the course and other courses organized by the SIB.
          For more information, please contact