A guided tour of the Trans-Proteomic Pipeline.
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.
Deutsch
Eric W
EW
Institute for Systems Biology, Seattle, WA, USA. edeutsch@systemsbiology.org
Mendoza
Luis
L
Shteynberg
David
D
Farrah
Terry
T
Lam
Henry
H
Tasman
Natalie
N
Sun
Zhi
Z
Nilsson
Erik
E
Pratt
Brian
B
Prazen
Bryan
B
Eng
Jimmy K
JK
Martin
Daniel B
DB
Nesvizhskii
Alexey I
AI
Aebersold
Ruedi
R
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