Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

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Deutsch, Eric W. ; Orchard, Sandra ; Binz, Pierre-Alain ; Bittremieux, Wout ; Eisenacher, Martin ; Hermjakob, Henning ; Kawano, Shin ; Lam, Henry ; Mayer, Gerhard ; Menschaert, Gerben ; Perez-Riverol, Yasset ; Salek, Reza M. ; Tabb, David L. ; Tenzer, Stefan ; Vizcaíno, Juan Antonio ; Walzer, Mathias ; Jones, Andrew R. (2017)
  • Publisher: American Chemical Society
  • Journal: Journal of Proteome Research, volume 16, issue 12, pages 4,288-4,298 (issn: 1535-3893, eissn: 1535-3907)
  • Related identifiers: doi: 10.1021/acs.jproteome.7b00370, handle: 10067/1450320151162165141, pmc: PMC5715286
  • Subject: Chemistry | Biology | proteomics | quality control | data standard | database | protein quantification | metabolomics | Perspective | mass spectrometry | protein identification | Computer. Automation | molecular interactions | bioinformatics software

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, co-chairs, 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. Further, 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 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.