The Proteomics Identifications database: 2010 update
Name
Vizcaino-2009-The Proteomics Identifications database.pdf
Size
3.1 MB
Format
Adobe PDF
Checksum (MD5)
5850c9ec64491bbe998b130a4e0bbd8e
Author(s)
Vizcaino, Juan Antonio
Cote, Richard
Reisinger, Florian
Barsnes, Harald
Foster, Joseph M.
Rameseder, Jonathan
Hermjakob, Henning
Martens, Lennart
Date Issued
November 2009
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
Vizcaino, J. A. et al. “The Proteomics Identifications Database: 2010 Update.” Nucleic Acids Research 38.Database (2009): D736–D742. Web.
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Computational and Systems Biology Program
Terms of Use
Creative Commons Attribution Non-Commercial
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1093/nar/gkp964
