共 52 条
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:
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.
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页码:1150 / 1159
页数:10
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