Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

被引：45

作者：

Vizcaino, Juan Antonio ^{[2
]}

Foster, Joseph M. ^{[2
]}

Martens, Lennart ^{[1
,3
]}

机构：

[1] Univ Ghent VIB, Dept Med Prot Res, B-9000 Ghent, Belgium

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

[3] Univ Ghent, Dept Biochem, B-9000 Ghent, Belgium

来源：

JOURNAL OF PROTEOMICS | 2010年 / 73卷 / 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：

Proteomics; Databases; Bioinformatics; Data standards; Repositories; MASS-SPECTROMETRY DATA; PEPTIDE IDENTIFICATIONS; PROTEIN IDENTIFICATION; PUBLIC REPOSITORY; NCBI PEPTIDOME; PRIDE; RESOURCE; SOFTWARE; SYSTEM; TANDEM;

D O I：

10.1016/j.jprot.2010.06.008

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Despite the fact that data deposition is not a generalised fact yet in the field of proteomics, several mass spectrometry (MS) based proteomics repositories are publicly available for the scientific community. The main existing resources are: the Global Proteome Machine Database (GPMDB), PeptideAtlas, the PRoteomics IDEntifications database (PRIDE), Tranche, and NCBI Peptidome. In this review the capabilities of each of these will be described, paying special attention to four key properties: data types stored, applicable data submission strategies, supported formats, and available data mining and visualization tools. Additionally, the data contents from model organisms will be enumerated for each resource. There are other valuable smaller and/or more specialized repositories but they will not be covered in this review. Finally, the concept behind the ProteomeXchange consortium, a collaborative effort among the main resources in the field, will be introduced. (C) 2010 Elsevier B.V. All rights reserved.

引用

页码：2136 / 2146

页数：11

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