Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

Eric W. Deutsch, Sandra Orchard, Pierre Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M. Salek, David L. Tabb, Stefan Tenzer, Juan Antonio Vizcaíno, Mathias Walzer, Andrew R. Jones

Research output: Contribution to journalReview articlepeer-review

73 Citations (Scopus)

Abstract

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

Original languageEnglish
Pages (from-to)4288-4298
Number of pages11
JournalJournal of Proteome Research
Volume16
Issue number12
DOIs
Publication statusPublished - 1 Dec 2017
Externally publishedYes

Keywords

  • bioinformatics software
  • data standard
  • database
  • mass spectrometry
  • metabolomics
  • molecular interactions
  • protein identification
  • protein quantification
  • proteomics
  • quality control

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