A guided tour of the Trans-Proteomic Pipeline

被引：585

作者：

Deutsch, Eric W. ^{[1
]}

Mendoza, Luis ^{[1
]}

Shteynberg, David ^{[1
]}

Farrah, Terry ^{[1
]}

Lam, Henry ^{[2
]}

Tasman, Natalie ^{[3
]}

Sun, Zhi ^{[1
]}

Nilsson, Erik ^{[3
]}

Pratt, Brian ^{[3
]}

Prazen, Bryan ^{[3
]}

Eng, Jimmy K. ^{[4
]}

Martin, Daniel B. ^{[1
]}

Nesvizhskii, Alexey I. ^{[5
,6
]}

Aebersold, Ruedi ^{[1
,7
,8
,9
]}

机构：

[1] Inst Syst Biol, Seattle, WA 98103 USA

[2] Hong Kong Univ Sci & Technol, Hong Kong, Hong Kong, Peoples R China

[3] Insilicos LLC, Seattle, WA USA

[4] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[5] Univ Michigan, Dept Pathol, Ann Arbor, MI 48109 USA

[6] Univ Michigan, Ctr Computat Med & Biol, Ann Arbor, MI 48109 USA

[7] ETH, Inst Mol Syst Biol, Zurich, Switzerland

[8] Univ Zurich, Fac Sci, Zurich, Switzerland

[9] Ctr Syst Physiol & Metab Dis, Zurich, Switzerland

来源：

PROTEOMICS | 2010年 / 10卷 / 06期

基金：

美国国家卫生研究院;

关键词：

Bioinformatics; MS/MS; Protein identification; TANDEM MASS-SPECTROMETRY; PEPTIDE IDENTIFICATION; STATISTICAL VALIDATION; PROTEIN IDENTIFICATION; DATABASE SEARCH; SPECTRAL DATA; SOFTWARE; STRATEGY; SYSTEM; MS/MS;

D O I：

10.1002/pmic.200900375

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of MS/MS data sets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by stable isotope ratios. We describe here the full workflow of the TPP and the tools therein, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.

引用

页码：1150 / 1159

页数：10

共 52 条

[1] Mass spectrometry-based proteomics [J].