A Guided Tour of the Trans-Proteomic Pipeline

By Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, T. Farrah, Henry H. N. Lam, Natalie I. Tasman, Zhi Sun, Erik J. Nilsson, Brian S. Pratt, B. Prazen and 4 more. Proteomics, 2010

753 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/7117adae60d6594822b5561892eb4888647cefce

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Citations in the corpus

Inaugural Article: The protein expression landscape of the Arabidopsis root (2012, positive): “All MS/MS spectra were processed and analyzed using the Trans-Proteomic Pipeline (TPP) (61).”
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, methodology): “[189] Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, et al.”
MSFragger: ultrafast and comprehensive peptide identification in shotgun proteomics (2017, methodology): “Tandem, Comet, and MSFragger output files were uniformly processed by PeptideProphet 54 via the Trans-Proteomic Pipeline (TPP v4.”
iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates* (2011, methodology): “For new users, the installation of the TPP is easy and is available on Windows, Linux, and OS X. Installation instructions are available at the Seattle Proteome Center web site: http://www.proteomecenter.org/software.php.”
Universal database search tool for proteomics (2014, neutral): “…this paper was prepared for a journal submission, MS-GF þ has already been integrated into the following pipelines and statistical modelling tools: Trans-Proteomics Pipeline 45 , Galaxy-P 46 , ProteoSuite 47 , IDPicker 11 , SearchGUI 48 , Scaffold 48 , ProteoSAFe, Skyline 49 and Percolator 10,50 .”
DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics (2015, methodology): “The initial search results from the search engines were first converted into pepXML format and then analyzed with PeptideProphet 23 via the TPP 44 (v4.”
mzML—a Community Standard for Mass Spectrometry Data (2010, background): “Tandem (29), Myrimatch (30), the Trans-Proteomic Pipeline (TPP) (31–33), and the Proteios Software Environment (34).”
OpenMS: a flexible open-source software platform for mass spectrometry data analysis (2016, methodology): “The OpenMS project is one of several software solutions addressing the computational challenges of MS-based proteomics, each contributing in different areas such as protein inference, peptide database search and file conversion 6,7,22,23 .”
LC-MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization Engine (2012, methodology): “For most mass spectrometers, file converters are freely available and maintained through the Seattle Proteome Center–Institute for Systems Biology through their Trans-Proteomic Pipeline (Deutsch et al., 2010).”
Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial (2018, neutral): “…developed that simplify and standardize this process and are available for example within Skyline (Egertson et al , 2015), PeakView (SCIEX), Spectro-naut Pulsar (further referred to as Spectronaut) (Bruderer et al , 2015) (Biognosys) and the Trans-Proteomic Pipeline (TPP) (Deutsch et al , 2010).”
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics (2015, methodology): “…number of individual tools for processing proteomics data [6] and some developed as pipelines [7,8], the Trans-Proteomic Pipeline (TPP; [9,10]) is the most widely used free and open-source complete suite of tools for processing shotgun proteomics data with statistical validation from…”