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Proteomics Identifications Database

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To cite PRIDE, please use the following reference:

Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O’Kelly G, Schoenegger A, Ovelleiro D, Perez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013.
Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-1069.PubMed PMID: 23203882;

PRIDE and PRIDE Tools Publications

Quality control in a proteomics data repository.
Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H.
Database 2012 Mar 20;2012:bas004.
PMID: 22434838

PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA.
Nat Biotechnol 2012 30(2): 135-137.
PMID: 22318026

PRIDE and “Database on Demand” as valuable tools for computational proteomics.
Vizcaíno JA, Reisinger F, Côté R, Martens L.
Methods Mol Biol 2011 696: 93-105.
PMID: 21063943

Submitting proteomics data to PRIDE using PRIDE Converter.
Barsnes H, Vizcaíno JA, Reisinger F, Eidhammer I, Martens L.
Methods Mol Biol 2011 694: 237-53.
PMID: 21082439

The Proteomics Identifications database: 2010 update.
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.
Nucleic Acids Res. 2010 38 (Database issue): D736-742.
PMID: 19906717

PRIDE: Data submission and analysis.
Vizcaíno JA, Reisinger F, Côté R, Martens L
Current Protocols in Protein Science, 2010 Chapter 25:Unit 25.4.
PMID: 20393974

A guide to the Proteomics Identifications Database proteomics data repository.
Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L.
Proteomics. 2009 Sep;9(18):4276-83.
PMID: 19662629

PRIDE Converter: making proteomics data-sharing easy.
Barsnes H, Vizcaíno JA, Eidhammer I, Martens L.
Nat Biotechnol. 2009 Jul;27(7):598-9. No abstract available.
PMID: 19587657

The PRIDE proteomics identifications database: data submission, query, and dataset comparison.
Jones P, Côté R.
Methods Mol Biol. 2008;484:287-303.
PMID: 18592187

Using the Proteomics Identifications Database (PRIDE).
Martens L, Jones P, Côté R.
Curr Protoc Bioinformatics. 2008 Mar;Chapter 13:Unit 13.8.
PMID: 18428683

PRIDE: new developments and new datasets.
Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H.
Nucleic Acids Res. 2008 Jan;36(Database issue):D878-83. Epub 2007 Nov 22.
PMID: 18033805

PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D659-63.
PMID: 16381953

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Hermjakob H, Apweiler R.
Expert Rev Proteomics. 2006 Feb;3(1):1-3. No abstract available.
PMID: 16445344

PRIDE: the proteomics identifications database.
Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R.
Proteomics. 2005 Aug;5(13):3537-45. Erratum in: Proteomics. 2005 Oct;5(15):4046.
PMID: 16041671

Other related publications by PRIDE team members

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
Griss J, Reisinger F, Hermjakob H, Vizcaíno JA.
Proteomics 2012 12(6): 795-798.
PMID: 22539430

jmzIdentML API: A java interface to the mzIdentML standard for peptide and protein identification data.
Reisinger F, Krishna R, Ghali F, Ríos D, Hermjakob H, Vizcaíno JA, Jones AR.
Proteomics 2012 12(6): 790-794.
PMID: 22539429

TraML--A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists.
Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY.
Mol Cell Proteomics 2012 Apr;11(4): R111.015040.
PMID: 22159873

Isoelectric point optimization using peptide descriptors and support vector machines.
Perez-Riverol Y, Audain E, Millan A, Ramos Y, Sanchez A, Vizcaíno JA, Wang R, Mueller M, Machado YJ, Betancourt LH, González LJ, Padrón G, Besada V.
J Proteomics 2012 75(7):2269-74.
PMID: 22326964

From proteomics data representation to public data flow: A report on the HUPO-PSI Workshop, September 2011, Geneva, Switzerland.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martínez-Bartolomé S, Vizcaíno JA, Hermjakob H.
Proteomics 2012 12(3):351-355.
PMID: 22290802

Enabling BioSharing – a report on the Annual Spring Workshop of the HUPO-PSI at EMBL-Heidelberg, Germany, April 11-13th 2011.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob, H.
Proteomics 2011 11(22): 4284-4290.
PMID: 22045680

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.
Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D.
Database 2011 Oct 23;2011:bar047.
PMID: 22025670

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB ‘complete proteome’ sets.
Griss J, Martín M, O’Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.
Proteomics 2011 11(22): 4434-4438.
PMID: 2193244

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.
Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA.
Mol Cell Proteomics 2011 10(9): M111.008490.
PMID: 21700957

Quality Control in Proteomics.
Martens L, Vizcaíno JA, Banks R.
Proteomics 2011 11(6): 1015-1016.
PMID: 21374817

Proteomic temporal profile of human brain endothelium post-oxidative stress.
Ning M, Sarracino DA, Kho AT, Guo S, Lee SR, Krastins B, Buonanno FS, Vizcaíno JA, Orchard S, McMullin D, Wang X, Lo EH.
Stroke 2011 42(1): 37-43.
PMID: 21164131

mzML--a community standard for mass spectrometry data.
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.
Mol Cell Proteomics 2011 Jan;10(1): R110.000133.
PMID: 20716697

Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.
Vizcaíno JA, Foster JM, Martens L.
J Proteomics 2010 73, 2136-2146.
PMID: 20615486

Organelle proteomics experimental designs and analysis.
Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS.
Proteomics 2010 10 (22): 3957-69
PMID: 21080489

The Ontology Lookup Service: Bigger and Better.
Côté R, Reisinger F, Martens L, Barsnes H, Vizcaíno JA, Hermjakob H.
Nucleic Acids Res 2010 38 (Web Server issue): W155-160.
PMID: 20460452

Charting online OMICS resources: a navigational chart for clinical researchers.
Vizcaíno JA, Mueller M, Hermjakob H, Martens L.
Proteomics Clin Appl 2009 3: 18-29.
PMID: 19587657

Database on Demand - an online tool for the custom generation of FASTA-formatted sequence databases.
Reisinger F, Martens L.
Proteomics. 2009 Sep;9(18):4421-4.
PMID: 19725076

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C.
Proteomics. 2009 Aug;9(15):3928-33.
PMID: 19637238

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ; HUPO Test Sample Working Group, Beardslee TA, Chappell T, Meredith G, Sheffield P, Gray P, Hajivandi M, Pope M, Predki P, Kullolli M, Hincapie M, Hancock WS, Jia W, Song L, Li L, Wei J, Yang B, Wang J, Ying W, Zhang Y, Cai Y, Qian X, He F, Meyer HE, Stephan C, Eisenacher M, Marcus K, Langenfeld E, May C, Carr SA, Ahmad R, Zhu W, Smith JW, Hanash SM, Struthers JJ, Wang H, Zhang Q, An Y, Goldman R, Carlsohn E, van der Post S, Hung KE, Sarracino DA, Parker K, Krastins B, Kucherlapati R, Bourassa S, Poirier GG, Kapp E, Patsiouras H, Moritz R, Simpson R, Houle B, Laboissiere S, Metalnikov P, Nguyen V, Pawson T, Wong CC, Cociorva D, Yates Iii JR, Ellison MJ, Lopez-Campistrous A, Semchuk P, Wang Y, Ping P, Elia G, Dunn MJ, Wynne K, Walker AK, Strahler JR, Andrews PC, Hood BL, Bigbee WL, Conrads TP, Smith D, Borchers CH, Lajoie GA, Bendall SC, Speicher KD, Speicher DW, Fujimoto M, Nakamura K, Paik YK, Cho SY, Kwon MS, Lee HJ, Jeong SK, Chung AS, Miller CA, Grimm R, Williams K, Dorschel C, Falkner JA, Martens L, Vizcaíno JA.
Nat Methods. 2009 May 17. [Epub ahead of print]
PMID: 19448641

Data standards and controlled vocabularies for proteomics.
Martens L, Palazzi LM, Hermjakob H.
Methods Mol Biol. 2008;484:279-86.
PMID: 18592186

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Mueller M, Vizcaíno JA, Jones P, Côté R, Thorneycroft D, Apweiler R, Hermjakob H, Martens L.
Proteomics. 2008 Mar;8(6):1138-48.
PMID: 18283668

Analyzing large-scale proteomics projects with latent semantic indexing.
Klie S, Martens L, Vizcaíno JA, Côté R, Jones P, Apweiler R, Hinneburg A, Hermjakob H.
J Proteome Res. 2008 Jan;7(1):182-91. Epub 2007 Nov 30.
PMID: 18047271

ISPIDER Central: an integrated database web-server for proteomics.
Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, Goble CA, Oliver SG, Stevens R, Zamboulis L, Martin N, Poulovassillis A, Jones P, Côté R, Hermjakob H, Pentony MM, Jones DT, Orengo CA, Hubbard SJ.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W485-90. Epub 2008 Apr 25.
PMID: 18440977

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W372-6. Epub 2008 May 8.
PMID: 18467421

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.
Orchard S, Hermjakob H.
Brief Bioinform. 2008 Mar;9(2):166-73. Epub 2007 Dec 7.
PMID: 18065433

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ.
Proteome Sci. 2007 Feb 1;5:4.
PMID: 17270041

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.
BMC Bioinformatics. 2007 Oct 18;8:401.
PMID: 17945017

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Martens L, Orchard S, Apweiler R, Hermjakob H.
Mol Cell Proteomics. 2007 Sep;6(9):1666-7. No abstract available.
PMID: 17766694

The minimum information about a proteomics experiment (MIAPE).
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H.
Nat Biotechnol. 2007 Aug;25(8):887-93. Review.
PMID: 17687369

Proteomics data validation: why all must provide data.
Martens L, Hermjakob H.
Mol Biosyst. 2007 Aug;3(8):518-22. Epub 2007 Jun 20.
PMID: 17639125

The PSI formal document process and its implementation on the PSI website.
Vizcaíno JA, Martens L, Hermjakob H, Julian RK, Paton NW.
Proteomics. 2007 Jul;7(14):2355-7.
PMID: 17570517

Annotating the human proteome: beyond establishing a parts list.
Mueller M, Martens L, Apweiler R.
Biochim Biophys Acta. 2007 Feb;1774(2):175-91. Epub 2006 Nov 30. Review.
PMID: 17223395

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Martens L, Orchard S, Apweiler R, Hermjakob H.
Mol Cell Proteomics. 2007 Sep;6(9):1666-7. No abstract available.
PMID: 17766694

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Hermjakob H, Apweiler R.
Expert Rev Proteomics. 2006 Feb;3(1):1-3. No abstract available.
PMID: 16445344

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
Orchard S, Kersey P, Hermjakob H, Apweiler R.
Comp Funct Genomics. 2003;4(1):16-9.
PMID: 18629102


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