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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp964
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The Proteomics Identifications database: 2010 update

Juan Antonio Vizcaíno1, Richard Côté1, Florian Reisinger1, Harald Barsnes2, Joseph M. Foster1, Jonathan Rameseder1,3, Henning Hermjakob1 and Lennart Martens1,*

1EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2Department of Informatics, University of Bergen, Norway and 3Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

*To whom correspondence should be addressed. Tel: +44 1223 492 610; Fax: +44 1223 494 484; Email: lennart.martens{at}ebi.ac.uk

Received September 10, 2009. Revised October 6, 2009. Accepted October 13, 2009.

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.


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