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The Proteomics Identifications database: 2010 update

Juan Antonio Vizcaíno, Richard Côté, Florian Reisinger, Harald Barsnes, Joseph M Foster, Jonathan Rameseder, Henning Hermjakob and Lennart Martens UGent (2010) NUCLEIC ACIDS RESEARCH. 38(suppl. 1). p.D736-D742
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PEPTIDE IDENTIFICATIONS, PUBLIC REPOSITORY, MS REPOSITORIES, PROTEIN, PRIDE, RESOURCE, GENERATION, PATHWAYS, PIPELINES, MASS-SPECTROMETRY
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
38
issue
suppl. 1
pages
D736 - D742
Web of Science type
Article
Web of Science id
000276399100116
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
7.836 (2010)
JCR rank
30/284 (2010)
JCR quartile
1 (2010)
ISSN
0305-1048
DOI
10.1093/nar/gkp964
language
English
UGent publication?
no
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
1258522
handle
http://hdl.handle.net/1854/LU-1258522
date created
2011-06-09 10:33:21
date last changed
2013-01-30 09:41:36
@article{1258522,
  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.},
  author       = {Vizca{\'i}no, Juan Antonio and C{\^o}t{\'e}, Richard and Reisinger, Florian and Barsnes, Harald and Foster, Joseph M and Rameseder, Jonathan and Hermjakob, Henning and Martens, Lennart},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {PEPTIDE IDENTIFICATIONS,PUBLIC REPOSITORY,MS REPOSITORIES,PROTEIN,PRIDE,RESOURCE,GENERATION,PATHWAYS,PIPELINES,MASS-SPECTROMETRY},
  language     = {eng},
  number       = {suppl. 1},
  pages        = {D736--D742},
  title        = {The Proteomics Identifications database: 2010 update},
  url          = {http://dx.doi.org/10.1093/nar/gkp964},
  volume       = {38},
  year         = {2010},
}

Chicago
Vizcaíno, Juan Antonio, Richard Côté, Florian Reisinger, Harald Barsnes, Joseph M Foster, Jonathan Rameseder, Henning Hermjakob, and Lennart Martens. 2010. “The Proteomics Identifications Database: 2010 Update.” Nucleic Acids Research 38 (suppl. 1): D736–D742.
APA
Vizcaíno, J. A., Côté, R., Reisinger, F., Barsnes, H., Foster, J. M., Rameseder, J., Hermjakob, H., et al. (2010). The Proteomics Identifications database: 2010 update. NUCLEIC ACIDS RESEARCH, 38(suppl. 1), D736–D742.
Vancouver
1.
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, et al. The Proteomics Identifications database: 2010 update. NUCLEIC ACIDS RESEARCH. 2010;38(suppl. 1):D736–D742.
MLA
Vizcaíno, Juan Antonio, Richard Côté, Florian Reisinger, et al. “The Proteomics Identifications Database: 2010 Update.” NUCLEIC ACIDS RESEARCH 38.suppl. 1 (2010): D736–D742. Print.