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PRIDE


NAR Molecular Biology Database Collection entry number 857
Jones P.1, Côté R.G.1, Martens L.2, Quinn A.F.1, Taylor C.F.1, Derache W.1, Hermjakob H.1 and Apweiler R.1
1EMBL Outstation - European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
1Dept. 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

Database Description

PRIDE, The ‘PRoteomics IDEntifications database’ [1,2] 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. 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 or mzData format. 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. Public PRIDE data sets and the open-source code base are available from http://www.ebi.ac.uk/pride.

Recent Developments

PRIDE has recently been translated from the default English into French, German and Korean. Language selection is automatic, depending on the locale setting of the users’ Internet browser. At the time of writing, PRIDE contains more than 1600 separate experiments, comprising almost 180,000 protein identifications and approximately 500,000 peptide identifications. PRIDE protein identifications can be queried through a Distributed Annotation System (DAS) [3] that provides details of the coordination of peptides

Acknowledgements

PRIDE is supported through BBSRC iSPIDER and HUPO Plasma Proteome Project funding as well as a EU Marie Curie fellowship.

References

1. Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R: PRIDE: the proteomics identifications database. Proteomics 2005, 5(13):3537-3545.
2. Jones P, Côté RG, Martens L, Quinn A, Taylor CF, Derache W, Hermjakob H, Apweiler R: PRIDE: A Public Repository of Protein and Peptide Identifications for the Proteomics Community. Nucleic Acids Research, in press.
3. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L: The distributed annotation system. BMC Bioinformatics 2001, 2:7.


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