The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

被引：1643

作者：

Vizcaino, Juan Antonio ^{[1
]}

Cote, Richard G. ^{[1
]}

Csordas, Attila ^{[1
]}

Dianes, Jose A. ^{[1
]}

Fabregat, Antonio ^{[1
]}

Foster, Joseph M. ^{[1
]}

Griss, Johannes ^{[1
]}

Alpi, Emanuele ^{[1
]}

Birim, Melih ^{[1
]}

Contell, Javier ^{[1
]}

O'Kelly, Gavin ^{[1
]}

Schoenegger, Andreas ^{[1
,3
]}

Ovelleiro, David ^{[1
]}

Perez-Riverol, Yasset ^{[1
,2
]}

Reisinger, Florian ^{[1
]}

Rios, Daniel ^{[1
]}

Wang, Rui ^{[1
]}

Hermjakob, Henning ^{[1
]}

机构：

[1] European Bioinformat Inst, EMBL Outstn, Cambridge, England

[2] Ctr Genet Engn & Biotechnol, Dept Prote, Havana, Cuba

[3] Austrian Acad Sci, CeMM Res Ctr Mol Med, A-1090 Vienna, Austria

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / D1期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

PUBLIC REPOSITORY; PROTEIN; STANDARD; PEPTIDE; CONVERTER; VISUALIZE; FRAMEWORK; PLATFORM; SYSTEM; API;

D O I：

10.1093/nar/gks1262

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.

引用

页码：D1063 / D1069

页数：7

共 53 条

[1] A home for raw proteomics data [J].

不详 .

NATURE METHODS, 2012, 9 (05) :419-419

[2] Reorganizing the protein space at the Universal Protein Resource (UniProt) [J].

Apweiler, Rolf ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Antunes, Ricardo ;

Casanova, Elisabet Barrera ;

Bely, Benoit ;

Bingley, Mark ;

Bower, Lawrence ;

Bursteinas, Borisas ;

Chan, Wei Mun ;

Chavali, Gayatri ;

Da Silva, Alan ;

Dimmer, Emily ;

Eberhardt, Ruth ;

Fazzini, Francesco ;

Fedotov, Alexander ;

Garavelli, John ;

Castro, Leyla Garcia ;

Gardner, Michael ;

Hieta, Reija ;

Huntley, Rachael ;

Jacobsen, Julius ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

Orchard, Sandra ;

Patient, Samuel ;

Pichler, Klemens ;

Poggioli, Diego ;

Pontikos, Nikolas ;

Pundir, Sangya ;

Rosanoff, Steven ;

Sawford, Tony ;

Sehra, Harminder ;

Turner, Edward ;

Wardell, Tony ;

Watkins, Xavier ;

Corbett, Matt ;

Donnelly, Mike ;

van Rensburg, Pieter ;

Goujon, Mickael ;

McWilliam, Hamish ;

Lopez, Rodrigo ;

Xenarios, Ioannis ;

Bougueleret, Lydie ;

Bridge, Alan ;

Poux, Sylvain ;

Redaschi, Nicole .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D71-D75

[3] PRIDE Converter: making proteomics data-sharing easy [J].

Barsnes, Harald ;

Vizcaino, Juan Antonio ;

Eidhammer, Ingvar ;

Martens, Lennart .

NATURE BIOTECHNOLOGY, 2009, 27 (07) :598-599

[4] The Ontology Lookup Service: bigger and better [J].

Cote, Richard ;

Reisinger, Florian ;

Martens, Lennart ;

Barsnes, Harald ;

Vizcaino, Juan Antonio ;

Hermjakob, Henning .

NUCLEIC ACIDS RESEARCH, 2010, 38 :W155-W160

[5] The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium [J].

Cote, Richard G. ;

Griss, Johannes ;

Dianes, Jose A. ;

Wang, Rui ;

Wright, James C. ;

van den Toorn, Henk W. P. ;

van Breukelen, Bas ;

Heck, Albert J. R. ;

Hulstaert, Niels ;

Martens, Lennart ;

Reisinger, Florian ;

Csordas, Attila ;

Ovelleiro, David ;

Perez-Rivevol, Yasset ;

Barsnes, Harald ;

Hermjakob, Henning ;

Vizcaino, Juan Antonio .

MOLECULAR & CELLULAR PROTEOMICS, 2012, 11 (12) :1682-1689

[6] jmzML, an open-source Java']Java API for mzML, the PSI standard for MS data [J].

Cote, Richard G. ;

Reisinger, Florian ;

Martens, Lennart .

PROTEOMICS, 2010, 10 (07) :1332-1335

[7] Open source system for analyzing, validating, and storing protein identification data [J].

Craig, R ;

Cortens, JP ;

Beavis, RC .

JOURNAL OF PROTEOME RESEARCH, 2004, 3 (06) :1234-1242

[8] Reactome: a database of reactions, pathways and biological processes [J].

Croft, David ;

O'Kelly, Gavin ;

Wu, Guanming ;

Haw, Robin ;

Gillespie, Marc ;

Matthews, Lisa ;

Caudy, Michael ;

Garapati, Phani ;

Gopinath, Gopal ;

Jassal, Bijay ;

Jupe, Steven ;

Kalatskaya, Irina ;

Mahajan, Shahana ;

May, Bruce ;

Ndegwa, Nelson ;

Schmidt, Esther ;

Shamovsky, Veronica ;

Yung, Christina ;

Birney, Ewan ;

Hermjakob, Henning ;

D'Eustachio, Peter ;

Stein, Lincoln .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D691-D697

[9] PRIDE: Quality control in a proteomics data repository [J].

Csordas, Attila ;

Ovelleiro, David ;

Wang, Rui ;

Foster, Joseph M. ;

Rios, Daniel ;

Vizcaino, Juan Antonio ;

Hermjakob, Henning .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2012,

[10] Top-down mass spectrometry: Recent developments, applications and perspectives [J].

Cui, Weidong ;

Rohrs, Henry W. ;

Gross, Michael L. .

ANALYST, 2011, 136 (19) :3854-3864

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