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
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
收藏
页码:1150 / 1159
页数:10
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