The ProteomeXchange consortium in 2026: making proteomics data FAIR
The ProteomeXchange consortium of proteomics resources (http://www.proteomexchange.org) was established to standardize open data practices in the mass spectrometry (MS)-based proteomics field. Here, we describe the main developments in ProteomeXchange in the last 3 years. The six member databases of ProteomeXchange, spread out in three different continents, are the PRIDE database, PeptideAtlas, MassIVE, jPOST, iProX, and Panorama Public. We provide updated data submission statistics, showcasing that the number of datasets submitted to ProteomeXchange resources has continued to accelerate every year. Through June 2025, 64 330 datasets had been submitted to ProteomeXchange resources, and from those, 30 097 (47%) just in the last 3 years. We also report on the improvements in the support for the standards developed by the Proteomics Standards Initiative, e.g. for Universal Spectrum Identifiers and for SDRF (Sample and Data Relationship Format)-Proteomics. Additionally, we highlight the increase in data reuse activities of public datasets, including targeted reanalyses of datasets of different proteomics data types, and the development of novel machine learning approaches. Finally, we summarize our plans for the near future, covering the development of resources for controlled-access human proteomics data, and for the support of non-MS proteomics approaches.
Authors
- Yasushi Ishihama (ORCID: https://orcid.org/0000-0001-7714-203X)
- Brian Connolly
- Jeremy Carver (ORCID: https://orcid.org/0000-0003-0384-8130)
- Deepti J Kundu (ORCID: https://orcid.org/0000-0003-2989-5971)
- Brendan MacLean (ORCID: https://orcid.org/0000-0002-9575-0255)
- Chakradhar Bandla (ORCID: https://orcid.org/0000-0001-6392-3759)
- Suresh Hewapathirana (ORCID: https://orcid.org/0000-0002-7862-5022)
- Shin Kawano (ORCID: https://orcid.org/0000-0002-7969-2972)
- Michael J. MacCoss (ORCID: https://orcid.org/0000-0003-1853-0256)
- Juan Antonio Vizcaíno (ORCID: https://orcid.org/0000-0002-3905-4335)
- Yasset Pérez‐Riverol (ORCID: https://orcid.org/0000-0001-6579-6941)
- Shujiro Okuda (ORCID: https://orcid.org/0000-0002-7704-8104)
- Eric W. Deutsch (ORCID: https://orcid.org/0000-0001-8732-0928)
- Luis Mendoza (ORCID: https://orcid.org/0000-0003-0128-8643)
- Selvakumar Kamatchinathan (ORCID: https://orcid.org/0009-0001-3644-2586)
- Zhi Sun (ORCID: https://orcid.org/0000-0003-3324-6851)
- Nuno Bandeira (ORCID: https://orcid.org/0000-0001-8385-3655)
- Tao Chen (ORCID: https://orcid.org/0000-0003-4110-0529)
- Yunping Zhu (ORCID: https://orcid.org/0000-0002-7320-7411)
- Vagisha Sharma (ORCID: https://orcid.org/0000-0003-1922-439X)
Institutions
- European Bioinformatics Institute (GB)
- University of Washington (US)
- Kyoto University (JP)
- Kyoto Pharmaceutical University (JP)
- Institute for Systems Biology (US)
- University of California San Diego (US)
- Bioinformatics Institute (RU)
- Beijing Proteome Research Center (CN)
- Research Organization of Information and Systems (JP)
- Kitasato University (JP)
- University of Montana (US)
- Niigata University (JP)
- Wellcome Trust (GB)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-11-06
- DOI
- https://doi.org/10.1093/nar/gkaf1146
- Citations
- 11
- Primary Topic
- Advanced Proteomics Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 8.32