Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite

The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a large complement of tools for spectrum processing, spectrum...

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Bibliographic Details
Published inJournal of proteome research Vol. 22; no. 2; pp. 615 - 624
Main Authors Deutsch, Eric W., Mendoza, Luis, Shteynberg, David D., Hoopmann, Michael R., Sun, Zhi, Eng, Jimmy K., Moritz, Robert L.
Format Journal Article
LanguageEnglish
Published United States American Chemical Society 03.02.2023
Subjects
Data Analysis
Mass Spectrometry
Probability
Proteomics - methods
Software
6.1.0 Parhelion
proteomics
PeptideProphet
ProteinProphet
computational proteomics
mass spectrometry
Trans-Proteomic Pipeline
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Summary:The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. Many of the tools include machine-learning modeling to extract the most information from data sets and build robust statistical models to compute the probabilities that derived information is correct. Here we present the latest information on the many TPP tools, and how TPP can be deployed on various platforms from personal Windows laptops to Linux clusters and expansive cloud computing environments. We describe tutorials on how to use TPP in a variety of ways and describe synergistic projects that leverage TPP. We conclude with plans for continued development of TPP.
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ISSN:1535-3893
1535-3907
DOI:10.1021/acs.jproteome.2c00624