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Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline

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Bioinformatics for Comparative Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 694))

Abstract

The LC-MS/MS shotgun proteomics workflow is widely used to identify and quantify sample peptides and proteins. The technique, however, presents a number of challenges for large-scale use, including the diverse raw data file formats output by mass spectrometers, the large false positive rate among peptide assignments to MS/MS spectra, and the loss of connectivity between identified peptides and the sample proteins that gave rise to them. Here we describe the Trans-Proteomic Pipeline, a freely available open source software suite that provides uniform analysis of LC-MS/MS data from raw data to quantified sample proteins. In a straightforward manner, users can extract MS/MS information from raw data of many instrument formats, submit them to search engines for peptide identification, validate the results to remove false hits, combine together results of multiple search engines, infer sample proteins that gave rise to the identified peptides, and perform quantitation at the peptide and protein levels.

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Acknowledgments

We would like to thank Eric Deutsch and Luis Mendoza for valuable discussions.

Author information

Authors and Affiliations

  1. Rosetta Biosoftware, Seattle, WA, USA

    Andrew Keller

  2. Institute for Systems Biology, Seattle, WA, USA

    David Shteynberg

Authors
  1. Andrew Keller
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  2. David Shteynberg
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Corresponding author

Correspondence to Andrew Keller .

Editor information

Editors and Affiliations

  1. Delaware Biotechnology Institute, Dept. Computer & Information Sciences, University of Delaware, Innovation Way 15, Newark, 19711, Delaware, USA

    Cathy H. Wu

  2. Delaware Biotechnology Institute, Dept. Computer & Information Sciences, University of Delaware, Innovation Way 15, Newark, 19711, Delaware, USA

    Chuming Chen

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Keller, A., Shteynberg, D. (2011). Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline. In: Wu, C., Chen, C. (eds) Bioinformatics for Comparative Proteomics. Methods in Molecular Biology, vol 694. Humana Press. https://doi.org/10.1007/978-1-60761-977-2_12

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  • DOI: https://doi.org/10.1007/978-1-60761-977-2_12

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-976-5

  • Online ISBN: 978-1-60761-977-2

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