Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0

Eric W. Deutsch*, Lydie Lane, Christopher M. Overall, Nuno Bandeira, Mark S. Baker, Charles Pineau, Robert L. Moritz, Fernando Corrales, Sandra Orchard, Jennifer E. Van Eyk, Young Ki Paik, Susan T. Weintraub, Yves Vandenbrouck, Gilbert S. Omenn

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    76 Citations (Scopus)


    The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on consensus-reaching discussions with the wider HPP community over the past year. The revised 3.0 guidelines address several major and minor identified gaps. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. The main checklist has been reorganized under headings and subitems, and related guidelines have been grouped. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well, and this timely update to version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ∼20 000 human proteins encoded by the human genome.

    Original languageEnglish
    Pages (from-to)4108-4116
    Number of pages9
    JournalJournal of Proteome Research
    Issue number12
    Early online date10 Oct 2019
    Publication statusPublished - 6 Dec 2019


    • B/D-HPP
    • C-HPP
    • false-discovery rates
    • guidelines
    • HPP
    • Human Proteome Project
    • mass spectrometry
    • standards
    • unicity checker
    • Universal Spectrum Identifier (USI)


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