From Peptidome to PRIDE: Public proteomics data migration at a large scale

被引：6

作者：

Csordas, Attila ^{[1
]}

Wang, Rui ^{[1
]}

Rios, Daniel ^{[1
]}

Reisinger, Florian ^{[1
]}

Foster, Joseph M. ^{[1
]}

Slotta, Douglas J. ^{[2
]}

Vizcaino, Juan Antonio ^{[1
]}

Hermjakob, Henning ^{[1
]}

机构：

[1] EBI, EMBL Outstn, Cambridge, England

[2] NIH, Natl Lib Med, Natl Ctr Biotechnol Informat, Bethesda, MD 20892 USA

来源：

PROTEOMICS | 2013年 / 13卷 / 10-11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：

Bioinformatics; Discontinuation; Mass spectrometry proteomics databases; Peptidome; PRIDE; PROTEIN; TOOLS;

D O I：

10.1002/pmic.201200514

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (NCBI) as a sibling resource to PRIDE, was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the Peptidome closure to ensure that data were not lost to the wider proteomics community by exporting it to PRIDE. As a result, data in the low terabyte range have been migrated from Peptidome to PRIDE and made publicly available under experiment accessions 17900-18271, representing 54 projects, approximate to 53 million mass spectra, approximate to 10 million peptide identifications, approximate to 650000 protein identifications, approximate to 1.1 million biologically relevant protein modifications, and 28 species, from more than 30 different labs.

引用

页码：1692 / 1695

页数：4

共 13 条

[1] 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

[2] 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

[3] Unimod: Protein modifications for mass spectrometry [J].

Creasy, DM ;

Cottrell, JS .

PROTEOMICS, 2004, 4 (06) :1534-1536

[4] 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,

[5] PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows [J].

Deutsch, Eric W. ;

Lam, Henry ;

Aebersold, Ruedi .

EMBO REPORTS, 2008, 9 (05) :429-434

[6] The Biomolecular Interaction Network Database in PSI-MI 2.5 [J].

Isserlin, Ruth ;

El-Badrawi, Rashad A. ;

Badery, Gary D. .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2011,

[7] The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results [J].

Jones, Andrew R. ;

Eisenacher, Martin ;

Mayer, Gerhard ;

Kohlbacher, Oliver ;

Siepen, Jennifer ;

Hubbard, Simon J. ;

Selley, Julian N. ;

Searle, Brian C. ;

Shofstahl, James ;

Seymour, Sean L. ;

Julian, Randall ;

Binz, Pierre-Alain ;

Deutsch, Eric W. ;

Hermjakob, Henning ;

Reisinger, Florian ;

Griss, Johannes ;

Vizcaino, Juan Antonio ;

Chambers, Matthew ;

Pizarro, Angel ;

Creasy, David .

MOLECULAR & CELLULAR PROTEOMICS, 2012, 11 (07)

[8] Broadening the horizon -: level 2.5 of the HUPO-PSI format for molecular interactions [J].

Kerrien, Samuel ;

Orchard, Sandra ;

Montecchi-Palazzi, Luisa ;

Aranda, Bruno ;

Quinn, Antony F. ;

Vinod, Nisha ;

Bader, Gary D. ;

Xenarios, Ioannis ;

Wojcik, Jerome ;

Sherman, David ;

Tyers, Mike ;

Salama, John J. ;

Moore, Susan ;

Ceol, Arnaud ;

Chatr-aryamontri, Andrew ;

Oesterheld, Matthias ;

Stuempflen, Volker ;

Salwinski, Lukasz ;

Nerothin, Jason ;

Cerami, Ethan ;

Cusick, Michael E. ;

Vidal, Marc ;

Gilson, Michael ;

Armstrong, John ;

Woollard, Peter ;

Hogue, Christopher ;

Eisenberg, David ;

Cesareni, Gianni ;

Apweiler, Rolf ;

Hermjakob, Henning .

BMC BIOLOGY, 2007, 5 (1)

[9] The PSI-MOD community standard for representation of protein modification data [J].

Montecchi-Palazzi, Luisa ;

Beavis, Ron ;

Binz, Pierre-Alain ;

Chalkley, Robert J. ;

Cottrell, John ;

Creasy, David ;

Shofstahl, Jim ;

Seymour, Sean L. ;

Garavelli, John S. .

NATURE BIOTECHNOLOGY, 2008, 26 (08) :864-866

[10] Interpretation of shotgun proteomic data - The protein inference problem [J].

Nesvizhskii, AI ;

Aebersold, R .

MOLECULAR & CELLULAR PROTEOMICS, 2005, 4 (10) :1419-1440

← 1 2 →