Protocol

Mass Spectrometry Data Analysis in Proteomics

Volume 367 of the series Methods in Molecular Biology pp 261-270

Proteomic Data Exchange and Storage

The Need for Common Standards and Public Repositories
  • Sandra OrchardAffiliated withEMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus
  • , Philip JonesAffiliated withEMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus
  • , Chris TaylorAffiliated withEMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus
  • , Weimin ZhuAffiliated withEMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus
  • , Randall K. JulianJr.Affiliated withEMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus
  • , Henning HermjakobAffiliated withEMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus
  • , Rolf ApweilerAffiliated withEMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus

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Abstract

The ever increasing volumes of proteomic data now being produced by laboratories across the world have resulted in major issues in data storage and accessibility. The further demands of multilaboratory initiatives has highlighted issues when collaborators cannot import data generated within the same project but generated by different hardware types and processed by laboratory-specific work flows and analyses packages. There is an increasing need for common data standards that will allow the interchange of data between different instrumentation, search engines, and between laboratory databases. This could then lead to the establishment of data repositories from where benchmark datasets could be accessed and reanalyzed.

The Human Proteome Organization is currently supporting efforts to establish such standards. The work of the Proteomics Standards Initiative has lead to the development of the mzData XML interchange standard and is now broadening its scope to produce a spectral analysis output format, mzIdent. Accompanying controlled vocabularies allow the accurate, while systematic, representation of metadata throughout both schema.

Key Words

Proteomics data standardization protein interaction mass spectrometry