title: A guided tour of the Trans-Proteomic Pipeline.
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.
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA. edeutsch@systemsbiology.org
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Luis
authors.initials: L
authors.lastname: Mendoza
authors.forename: David
authors.initials: D
authors.lastname: Shteynberg
authors.forename: Terry
authors.initials: T
authors.lastname: Farrah
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.forename: Natalie
authors.initials: N
authors.lastname: Tasman
authors.forename: Zhi
authors.initials: Z
authors.lastname: Sun
authors.forename: Erik
authors.initials: E
authors.lastname: Nilsson
authors.forename: Brian
authors.initials: B
authors.lastname: Pratt
authors.forename: Bryan
authors.initials: B
authors.lastname: Prazen
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Martin
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D016247:Information Storage and Retrieval; D007553:Isotope Labeling; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software; D053719:Tandem Mass Spectrometry