ProteomeXchange
ProteomeXchange coordinates submission and standardization of mass spectrometry (MS) proteomics data to enable integration, sharing, and reuse of proteomic datasets across major repositories for biological and clinical research.
Key Features:
- Standardization and Coordination: Provides a unified framework for submitting MS proteomics data to ensure consistent formatting and interoperability across repositories.
- Global Consortium: Integrates six member resources—PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX, and Panorama Public—that collectively support dataset submission and dissemination.
- Data Submission Growth: As of June 2022, over 34,233 datasets have been submitted to ProteomeXchange, including 20,062 contributions in the preceding three years.
- Universal Spectrum Identifiers: Implements Universal Spectrum Identifiers to improve spectrum-level traceability and cross-resource referencing.
- Enhanced Metadata Annotations: Captures expanded experimental metadata annotations to provide contextual information that facilitates dataset reuse and analysis.
- Data Re-use and Integration: Promotes reuse of public datasets and integration with other bioinformatics resources to enable development of new data resources.
- Sensitive Data Management: Addresses management of sensitive human (clinical) proteomics data by applying data management practices intended to protect privacy while enabling scientific use.
Scientific Applications:
- Basic and mechanistic research: Provides access to MS proteomics datasets for studies of biological processes and disease mechanisms.
- Clinical and translational research: Supports clinical studies that can inform diagnostics and therapeutic strategies through access to curated proteomic data.
- Data reuse and resource development: Enables reanalysis and integration of public datasets to support creation of new data resources and secondary analyses.
Methodology:
Uses standardized submission frameworks, Universal Spectrum Identifiers, and enhanced experimental metadata annotations to integrate MS proteomics datasets into member repositories PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX, and Panorama Public and to support management of sensitive human (clinical) proteomics data.
Topics
Collections
Details
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 1/17/2017
- Last Updated:
- 1/30/2023
Operations
Publications
Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz P, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus H, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnology. 2014;32(3):223-226. doi:10.1038/nbt.2839. PMID:24727771. PMCID:PMC3986813.
Hermjakob H, Apweiler R. The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Review of Proteomics. 2006;3(1):1-3. doi:10.1586/14789450.3.1.1.
Deutsch EW, Bandeira N, Perez-Riverol Y, Sharma V, Carver JJ, Mendoza L, Kundu DJ, Wang S, Bandla C, Kamatchinathan S, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Research. 2022;51(D1):D1539-D1548. doi:10.1093/nar/gkac1040. PMID:36370099. PMCID:PMC9825490.