A guided tour of the Trans-Proteomic Pipeline

Eric W. Deutsch; Luis Mendoza; David Shteynberg; Terry Farrah; Henry Lam; Natalie Tasman; Zhi Sun; Erik Nilsson; Brian Pratt; Bryan Prazen; Jimmy K. Eng; Daniel B. Martin; Alexey I. Nesvizhskii; Ruedi Aebersold

doi:10.1002/pmic.200900375

A guided tour of the Trans-Proteomic Pipeline

Eric W. Deutsch, Luis Mendoza, David Shteynberg, Terry Farrah, Henry Lam, Natalie Tasman, Zhi Sun, Erik Nilsson, Brian Pratt, Bryan Prazen, Jimmy K. Eng, Daniel B. Martin, Alexey I. Nesvizhskii, Ruedi Aebersold

Research output: Contribution to journal › Review article › peer-review

637 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	1150-1159
Number of pages	10
Journal	Proteomics
Volume	10
Issue number	6
DOIs	https://doi.org/10.1002/pmic.200900375
Publication status	Published - 1 Mar 2010
Externally published	Yes

Keywords

Bioinformatics
MS/MS
Protein identification

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10.1002/pmic.200900375

Cite this

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AU - Shteynberg, David

AU - Farrah, Terry

AU - Lam, Henry

AU - Tasman, Natalie

AU - Sun, Zhi

AU - Nilsson, Erik

AU - Pratt, Brian

AU - Prazen, Bryan

AU - Eng, Jimmy K.

AU - Martin, Daniel B.

AU - Nesvizhskii, Alexey I.

AU - Aebersold, Ruedi

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A guided tour of the Trans-Proteomic Pipeline

Abstract

Keywords

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