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A guided tour of the Trans‐Proteomic Pipeline
Author(s) -
Deutsch Eric W.,
Mendoza Luis,
Shteynberg David,
Farrah Terry,
Lam Henry,
Tasman Natalie,
Sun Zhi,
Nilsson Erik,
Pratt Brian,
Prazen Bryan,
Eng Jimmy K.,
Martin Daniel B.,
Nesvizhskii Alexey I.,
Aebersold Ruedi
Publication year - 2010
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200900375
Subject(s) - pipeline (software) , workflow , computer science , suite , software , software suite , data mining , software engineering , set (abstract data type) , database , programming language , archaeology , history
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.