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A guided tour of the Trans‐Proteomic Pipeline

2010; Wiley; Volume: 10; Issue: 6 Linguagem: Inglês

10.1002/pmic.200900375

1615-9861

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

Metabolomics and Mass Spectrometry Studies

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.