A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

被引：36

作者：

Gonzalez-Galarza, Faviel F. ^{[1
]}

Lawless, Craig ^{[2
]}

Hubbard, Simon J. ^{[2
]}

Fan, Jun ^{[3
]}

Bessant, Conrad ^{[3
]}

Hermjakob, Henning ^{[4
]}

Jones, Andrew R. ^{[1
]}

机构：

[1] Univ Liverpool, Inst Integrat Biol, Liverpool L69 7ZB, Merseyside, England

[2] Univ Manchester, Fac Life Sci, Manchester, Lancs, England

[3] Cranfield Univ, Bioinformat Grp, Cranfield MK43 0AL, Beds, England

[4] EMBL European Bioinformat Inst, Hinxton, England

来源：

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY | 2012年 / 16卷 / 09期

基金：

英国生物技术与生命科学研究理事会;

关键词：

MASS-SPECTROMETRY DATA; MULTIPLEXED ABSOLUTE QUANTIFICATION; COMPLEX PROTEIN MIXTURES; LC-MS; PEPTIDE IDENTIFICATION; LIQUID-CHROMATOGRAPHY; COMPUTATIONAL METHODS; STATISTICAL-MODEL; MULTI-Q; Q WEB;

D O I：

10.1089/omi.2012.0022

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology.

引用

页码：431 / 442

页数：12

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