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PMID: 19906717 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The Proteomics Identifications database: 2010 update.

Nucleic acids research ·Vol. 38 ·No. Database issue ·2010-01-00 ·Pages D736-42

Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L

Abstract

The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 million peptides and over 50 million spectra by September 2009. We here describe several new and improved features in PRIDE, including the revised submission process, which now includes direct submission of fragment ion annotations. Correspondingly, it is now possible to visualize spectrum fragmentation annotations on tandem mass spectra, a key feature for compliance with journal data submission requirements. We also describe recent developments in the PRIDE BioMart interface, which now allows integrative queries that can join PRIDE data to a growing number of biological resources such as Reactome, Ensembl, InterPro and UniProt. This ability to perform extremely powerful across-domain queries will certainly be a cornerstone of future bioinformatics analyses. Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium.

MeSH Terms
Animals Computational Biology/methods,trends Databases, Genetic Databases, Nucleic Acid Databases, Protein Humans Information Storage and Retrieval/methods Internet Ions Mass Spectrometry/methods Protein Structure, Tertiary Proteomics/methods Software
Chemicals
Ions
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Vizcaíno Juan Antonio
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Côté Richard
Reisinger Florian
Barsnes Harald
Foster Joseph M
Rameseder Jonathan
Hermjakob Henning
Martens Lennart
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkp964
Published
2010-01-00
Epub
2009-00-11
Pages
D736-42
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2808904
Subset
IM
Grants
Wellcome Trust · WT085949MA · United Kingdom
External Links
PubMed source DOI: 10.1093/nar/gkp964 PMC Full Text View journal details
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