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Wiley, Proteomics, 6(10), p. 1150-1159, 2010

DOI: 10.1002/pmic.200900375

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A Guided Tour of the Trans-Proteomic Pipeline

Journal article published in 2010 by Eric W. Deutsch ORCID, Luis Mendoza, David Shteynberg, Terry Farrah, Henry Lam ORCID, Natalie Tasman, Zhi Sun, Erik Nilsson, Brian Pratt, Bryan Prazen, Jimmy K. Eng, Daniel B. Martin, Alexey I. Nesvizhskii, Ruedi Aebersold
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of tandem mass spectrometry datasets. 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 dataset, demonstrating that the set up and use of the tools is straightforward and well supported and does not require specialized informatics resources or knowledge.