PRIDE (repository)

PRIDE (repository)
Name	PRIDE
Type	Repository
Country	United Kingdom
Established	2004
Discipline	Proteomics

PRIDE (repository) is a public proteomics data repository that archives mass spectrometry-based proteomics datasets, spectral libraries, and associated metadata. It serves as a central resource for researchers in proteomics, biochemistry, molecular biology, and systems biology seeking to deposit, share, and reanalyze raw and processed proteomics data. PRIDE supports integration with major bioinformatics resources, community standards, and large-scale projects across Europe, North America, and Asia.

Overview

PRIDE is operated by a consortium that includes the European Bioinformatics Institute, collaborating partners such as the European Molecular Biology Laboratory, project participants from the Wellcome Trust, contributors from the Max Planck Society, and links to resources like UniProt, Ensembl, Reactome, and IntAct. The repository accepts submissions from laboratories involved with initiatives such as the Human Proteome Project, the ProteomeXchange Consortium, the Cancer Moonshot, and platforms used by groups at institutions including Harvard University, Massachusetts Institute of Technology, Stanford University, University of Oxford, and University of Cambridge. PRIDE interoperates with databases like PeptideAtlas, GPMDB, MassIVE, and analytical tools developed at centers including the European Molecular Biology Laboratory–European Bioinformatics Institute, European Research Council funded groups, and teams associated with the National Institutes of Health.

History

PRIDE was created in the early 2000s amid community efforts such as the Human Proteome Organization and early standards work led by organizations including the Proteomics Standards Initiative and funders like the Wellcome Trust. Initial development involved teams at the European Bioinformatics Institute and partners in projects supported by the European Commission and the Marie Skłodowska-Curie Actions. Over time PRIDE expanded through collaborations with the ProteomeXchange Consortium, integrations with UniProtKB, and interoperability work with groups at National Center for Biotechnology Information and European Molecular Biology Laboratory. Key milestones include adoption by large consortia such as the Human Proteome Project, participation in benchmarking with the Critical Assessment of Proteomics Informatics, and linkage to translational efforts like the Cancer Research UK initiatives.

Data content and submission

PRIDE accepts mass spectrometry raw files, processed results, identification lists, quantification tables, and spectral libraries generated by instruments made by vendors such as Thermo Fisher Scientific, Bruker, AB Sciex, and Waters Corporation. Submitters include investigators from institutions like Johns Hopkins University, Yale University, University of California, San Francisco, Cold Spring Harbor Laboratory, and laboratories collaborating with consortia such as ENCODE and International Human Epigenome Consortium. The submission workflow uses standards developed by the Proteomics Standards Initiative and metadata schemas aligned with resources including BioSamples Database, ArrayExpress, and European Genome-phenome Archive, facilitating links to projects at Wellcome Sanger Institute, Francis Crick Institute, and clinical cohorts from hospitals affiliated with Mayo Clinic and Cleveland Clinic.

Access and tools

Users access PRIDE through web interfaces maintained by the European Bioinformatics Institute and programmatic APIs used by developers at companies like Illumina and academic groups at ETH Zurich, Imperial College London, and Karolinska Institutet. Visualization and reanalysis tools integrated with PRIDE include software from the OpenMS project, search engines such as Mascot and MaxQuant, spectral library tools like SpectraST, and pipelines developed by groups at European Molecular Biology Laboratory, University of Washington, and European Bioinformatics Institute. PRIDE datasets are discoverable via resources like Google Dataset Search, indexed by aggregators such as ELIXIR, and linked to pathway databases including KEGG, MetaCyc, and WikiPathways.

Standards and interoperability

PRIDE adopts community standards from the Proteomics Standards Initiative, including formats like mzML and mzIdentML, and collaborates with the ProteomeXchange Consortium for dataset exchange. Interoperability efforts connect PRIDE to sequence resources like UniProt, annotation services at InterPro, ontology initiatives such as the Gene Ontology and Experimental Factor Ontology, and identifier mapping projects like Identifier.org. The repository participates in metadata standardization with organizations such as BioSamples Database, ELIXIR, and policy discussions involving the European Commission and the National Institutes of Health for data sharing and reproducibility.

Impact and usage

PRIDE has enabled reuse of datasets in research at institutions including Princeton University, Columbia University, University of Toronto, Peking University, University of Tokyo, and enabled studies published in journals like Nature, Science, Cell, Nature Communications, and Journal of Proteome Research. The repository supports large-scale meta-analyses by consortia such as the Human Proteome Project and translational studies in collaboration with Cancer Research UK, European Society for Medical Oncology, and clinical researchers at Mount Sinai Health System. PRIDE's datasets have been cited in projects from the International Cancer Genome Consortium and integrated into resources like GTex, Pan-Cancer Analysis of Whole Genomes, and pathway reconstructions at Reactome.

Governance and funding

PRIDE is governed by teams at the European Bioinformatics Institute with advisory roles from stakeholders including members of the ProteomeXchange Consortium, funders such as the Wellcome Trust, the European Commission, the European Research Council, and national agencies like the Medical Research Council and the National Institutes of Health. Operational funding and development have been supported through grants from programs such as Horizon 2020, collaborations with the Human Proteome Organization, and bilateral partnerships with institutions including the European Molecular Biology Laboratory and the Wellcome Sanger Institute.

Category:Proteomics databases