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Nucleic Acids Research 2006 34(Database Issue):D659-D663; doi:10.1093/nar/gkj138
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Nucleic Acids Research, 2006, Vol. 34, Database issue D659-D663
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

PRIDE: a public repository of protein and peptide identifications for the proteomics community

Philip Jones1,*, Richard G. Côté1, Lennart Martens2, Antony F. Quinn1, Chris F. Taylor1, William Derache1, Henning Hermjakob1 and Rolf Apweiler1

1EMBL Outstation, European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK 2Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology, Faculty of Medicine and Health Sciences, Ghent University, Rommelaere Institute Building D, A. Baertsoenkaai 3, B-9000 Ghent, Belgium

*To whom correspondence should be addressed. Tel: +44 1223 492610; Fax: +44 1223 494468; Email: pjones{at}ebi.ac.uk

Received August 15, 2005. Revised October 27, 2005. Accepted October 27, 2005.

PRIDE, the ‘PRoteomics IDEntifications database’ (http://www.ebi.ac.uk/pride) is a database of protein and peptide identifications that have been described in the scientific literature. These identifications will typically be from specific species, tissues and sub-cellular locations, perhaps under specific disease conditions. Any post-translational modifications that have been identified on individual peptides can be described. These identifications may be annotated with supporting mass spectra. At the time of writing, PRIDE includes the full set of identifications as submitted by individual laboratories participating in the HUPO Plasma Proteome Project and a profile of the human platelet proteome submitted by the University of Ghent in Belgium. By late 2005 PRIDE is expected to contain the identifications and spectra generated by the HUPO Brain Proteome Project. Proteomics laboratories are encouraged to submit their identifications and spectra to PRIDE to support their manuscript submissions to proteomics journals. Data can be submitted in PRIDE XML format if identifications are included or mzData format if the submitter is depositing mass spectra without identifications. PRIDE is a web application, so submission, searching and data retrieval can all be performed using an internet browser. PRIDE can be searched by experiment accession number, protein accession number, literature reference and sample parameters including species, tissue, sub-cellular location and disease state. Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML.


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