Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

Abstract

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics.

The 2023 Report on the Proteome from the HUPO Human Proteome Project

“…The HPP organization includes 25 teams by nuclear and mitochondrial chromosomes, 16 teams based on biological and clinical categories, and four resource pillars . The work is supported by advances in data formats and standards by the HUPO Proteome Standards Initiative , (HUPO-PSI), ProteomeXchange Consortium data repositories, and the concomitant growth of UniProtKB, Swiss-Prot, and neXtProt.…”

The Importance, Challenges, and Possible Solutions for Sharing Proteomics Data While Safeguarding Individuals’ Privacy

“…The data shared on each repository is accessible from ProteomeCentral ( proteomecentral.proteomexchange.org ). In a separate effort, Human Proteome Organization-Proteomics Standards Initiative (HUPO-PSI) published the standard for MS raw data as mzML, peptide or protein identification data, and quantification data as mzTab ( 52 , 53 ). The standard data formats and data submission guidelines are being followed in each repository, which has made MS-based proteomics more accessible and useful for the scientific community.…”

Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite

“…Although the TPP does not use the Proteomics Standards Initiative − (PSI) standard format mzIdentML internally, the final output of a TPP analysis may be exported to mzIdentML 1.2 via the TPP tool tpp2mzid for deposition to ProteomeXchange − repositories or for use with other mzIdentML-supporting tools. In the other direction, users may use the ProteoWizard idconvert tool (bundled with TPP) to convert externally acquired mzIdentML files to pepXML for further TPP processing.…”