Published December 1, 2017 | Version v1
Journal article Open

Proteomics Standards Initiative: Fifteen years of progress and future work

  • 1. Institute for Systems Biology, Seattle, Washington 98109, United States
  • 2. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
  • 3. CHUV Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
  • 4. Department of Mathematics and Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerp, Belgium
  • 5. Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
  • 6. Database Center for Life Science, Joint Support Center for Data Science Research, Research Organization of Information and Systems, Kashiwa, Chiba 277-0871, Japan
  • 7. Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, P. R. China
  • 8. Lab of Bioinformatics and Computational Genomics (BioBix), Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
  • 9. SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
  • 10. Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, 55131 Mainz, Germany
  • 11. Institute of Integrative Biology, University of Liverpool, South Wirral L64 4AY, United Kingdom


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.


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