How to submit MS proteomics data to ProteomeXchange via the PRIDE database

被引：41

作者：

Ternent, Tobias ^{[1
]}

Csordas, Attila ^{[1
]}

Qi, Da ^{[2
]}

Gomez-Baena, Guadalupe ^{[2
]}

Beynon, Robert J. ^{[2
]}

Jones, Andrew R. ^{[2
]}

Hermjakob, Henning ^{[1
]}

Vizcaino, Juan Antonio ^{[1
]}

机构：

[1] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Cambridge CB10 1SD, England

[2] Univ Liverpool, Inst Integrat Biol, Liverpool L69 3BX, Merseyside, England

来源：

PROTEOMICS | 2014年 / 14卷 / 20期

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会;

关键词：

Bioinformatics; Data standard; Data submission; Data visualization; Proteomics repositories; OPEN-SOURCE SOFTWARE; PEPTIDE IDENTIFICATION; DATA SUBMISSION; TOOLS; FRAMEWORK; STANDARD; PLATFORM; LIBRARY; VIEWER;

D O I：

10.1002/pmic.201400120

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The ProteomeXchange (PX) consortium has been established to standardize and facilitate submission and dissemination of MS-based proteomics data in the public domain. In the consortium, the PRIDE database at the European Bioinformatics Institute, acts as the initial submission point of MS/MS data sets. In this manuscript, we explain step by step the submission process of MS/MS data sets to PX via PRIDE. We describe in detail the two available workflows: 'complete' and 'partial' submissions, together with the available tools to streamline the process. Throughout the manuscript, we will use one example data set containing identification and quantification data, which has been deposited in PRIDE/ProteomeXchange with the accession number PXD000764 (http://proteomecentral.proteomexchange.org/dataset/PXD000764).

引用

收藏

页码：2233 / 2241

页数：9

相关论文

共 24 条

[1] The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards [J].

Alberto Medina-Aunon, J. ;

Martinez-Bartolome, Salvador ;

Lopez-Garcia, Miguel A. ;

Salazar, Emilio ;

Navajas, Rosana ;

Jones, Andrew R. ;

Paradela, Alberto ;

Albar, Juan P. .

MOLECULAR & CELLULAR PROTEOMICS, 2011, 10 (10)

[2] MS-Viewer: A Web-based Spectral Viewer for Proteomics Results [J].

Baker, Peter R. ;

Chalkley, Robert J. .

MOLECULAR & CELLULAR PROTEOMICS, 2014, 13 (05) :1392-1396

[3] 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

[4] 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

[5]

Csordas A., 2012, DATABASE, V2012

[6] Pepitome: Evaluating Improved Spectral Library Search for Identification Complementarity and Quality Assessment [J].

Dasari, Surendra ;

Chambers, Matthew C. ;

Martinez, Misti A. ;

Carpenter, Kristin L. ;

Ham, Amy-Joan L. ;

Vega-Montoto, Lorenzo J. ;

Tabb, David L. .

JOURNAL OF PROTEOME RESEARCH, 2012, 11 (03) :1686-1695

[7] TagRecon: High-Throughput Mutation Identification through Sequence Tagging [J].

Dasari, Surendra ;

Chambers, Matthew C. ;

Slebos, Robbert J. ;

Zimmerman, Lisa J. ;

Ham, Amy-Joan L. ;

Tabb, David L. .

JOURNAL OF PROTEOME RESEARCH, 2010, 9 (04) :1716-1726

[8] 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

[9] PASSEL: The PeptideAtlas SRM experiment library [J].

Farrah, Terry ;

Deutsch, Eric W. ;

Kreisberg, Richard ;

Sun, Zhi ;

Campbell, David S. ;

Mendoza, Luis ;

Kusebauch, Ulrike ;

Brusniak, Mi-Youn ;

Huettenhain, Ruth ;

Schiess, Ralph ;

Selevsek, Nathalie ;

Aebersold, Ruedi ;

Moritz, Robert L. .

PROTEOMICS, 2012, 12 (08) :1170-1175

[10] A posteriori quality control for the curation and reuse of public proteomics data [J].

Foster, Joseph M. ;

Degroeve, Sven ;

Gatto, Laurent ;

Visser, Matthieu ;

Wang, Rui ;

Griss, Johannes ;

Apweiler, Rolf ;

Martens, Lennart .

PROTEOMICS, 2011, 11 (11) :2182-2194