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Mass Spectrometry Standards Working Group

Updated: 2024-02-22

About us

The PSI Mass Spectrometry Standards Working Group defines community guidelines, data formats, and controlled vocabularies to facilitate data exchange and archiving in the field of mass spectrometry-based proteomics.

Current projects

  • Developing the mzSpecLib format, which will provide a PSI-standardized model and implementation for storing metadata-rich spectral libraries.
  • Developing mzPAF, a fragmentation peak annotation format, which will provide a PSI-standardized model and format for annotating the interpretations of fragment ion peaks in tandem MS spectra.
  • Extending the mzML format to support ion mobility MS and data independent acquisition (DIA) MS in a consistent and more efficient way. mzML 1.1.0 was released on June 1, 2009 and has been stable since then.

Completed Standards

    • The Universal Spectrum Identifier (USI) has been developed as a mechanism to identify and access any spectrum that has been deposited into one of the ProteomeXchange public data repositories. Work is still ongoing to define its use for accessing spectra in public spectral libraries.
    • The PSI Extended FASTA Format (PEFF) standard provides a FASTA-like format for storing amino acid and nucleotide sequences in a fully standardized manner, along with support for encoding sequence variants, post-translational modifications, and other sequence processing.
    • The ProForma 2.0 standard provides a fully standardized mechanism for encoding amino acid sequences along with their mass modifications, either as peptidoforms or full-length proteoforms.
    • The proBAM and proBed standards describe formats to encode proteomics peptidoform identifications in manners that are compatible with the popular BAM and BED formats widely used by the genomics community and genomics tools.
    • The TraML format has been developed as a standardized format for the exchange and transmission of transition lists for selected reaction monitoring (SRM) experiments. This specification has been been accepted through the PSI document process and is complete.
    • The MIAPE-MS, MIAPE-MSI, and MIAPE-Quant standards provide a standard set of guidelines for describing several components of the Minimum Information About a Proteomics Experiment (MIAPE).
    • The mzData standard is now deprecated in favor of mzML.

    Note: the mzIdentML, mzQuantML, and mzTAB standards are managed by the Proteomics Informatics Working Group.

    Group Structure (2024)

    Role  Name
    Chair Eric Deutsch, Institute for Systems Biology
    Co-chairs Pierre-Alain Binz, Centre Universitaire Hospitalier Vaudois CHUV,
    Henry Lam, Hong Kong University of Science and Technology
    Secretary  – currently vacant – 
    MIAPE Pierre-Alain Binz, Centre Universitaire Hospitalier Vaudois CHUV
    Ontology Co-ordinators Joshua Klein, Boston University 

    Other Active Working Group Members

    • Nuno Bandeira, University of California San Diego
    • Wout Bittremieux, Antwerp University
    • Jeremy Carver, University of California San Diego
    • Matthew Chambers, Bioinformatics Consultant
    • Tine Claeys, Ghent University
    • Ralf Gabriels, Ghent University
    • Helge Hecht, Masaryk University
    • Nils Hoffmann, Forschungszentrum Jülich GmbH
    • Andy Jones, University of Liverpool
    • Shin Kawano, Toyama University of International Studies
    • Tytus Mak, US National Institute for Standards and Technology (NIST)
    • Luis Mendoza, Institute for Systems Biology (ISB)
    • Ben Neely, US National Institute for Standards and Technology (NIST)
    • Thomas Payne, European Bioinformatics Institute (EBI)
    • Yasset Perez-Riverol, European Bioinformatics Institute (EBI)
    • Douwe Schulte, Utrecht University
    • Jim Shofstahl, Thermo Fisher Scientific
    • Tomi Suomi, University of Turku
    • Tim Van Den Bossche, Ghent University
    • Juan Antonio Vizcaíno, European Bioinformatics Institute (EBI)
    • Yunping Zhu, National Center for Protein Sciences (Beijing)


    Controlled Vocabulary: The PSI-MS CV

    The PSI-MS Controlled Vocabulary is developed in common with the PSI Proteomics Informatics Working Group. It consists of a large collection of structured terms covering description and use of mass spectrometry instrumentation as well as protein identification and quantitation software. The source of the terms are multiple: they include vocabulary and definitions in chapter 12 of the IUPAC nomenclature book, instrument and software vendors and developers and other user-submitted terms. Although its structure and use is linked to mzML, mzIdentML, mzQuantML, mzSpecLib, TraML, etc. it is dynamically maintained in a OBO format.

    The latest version of the PSI-MS CV is available here.

    To request new CV terms to be added to the PSI-MS Controlled Vocabulary, please use the psidev-vocab mailing list.

    More information on PSI CVs can be found here.

    We also provide a mail discussion list for mass spectroscopy standard development.
    You can mail to this list at, or subscribe/unsubscribe.