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The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.



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Authors and Contributors

See TPP:Authors and Contributors

Getting the software

For support both during and after installation, you are encouraged to consult the SPC Tools newsgroups:

Installing on a Windows System

The Windows version of TPP is provided as a pre-built binary self-installing executable which can be downloaded from the SourceForge site here. There also detailed instructions on how to install all prerequisites for TPP in the Windows installation guide.

Source Code Installation (For Linux systems)

The latest source code package can be found here, on the Sashimi project site on SourceForge. This is gzipped tar archive that can be unpacked using tools such as tar, 7-zip, or WinZip. Details on how to compile TPP can be found in the README and INSTALL_LINUX files found in the top level directory of the package.

Advanced Topic: building the TPP from source on Windows

NOTE: These advanced topics are for developers. Windows users can download and run the TPP Windows installer, which includes everything needed to run the TPP.


Please Note: The TPP is not currently officially supported on Mac OSX. This means that we cannot respond to installation or usage help requests. Users, however, are encouraged to post to the spctools-discuss newsgroup to seek help from the community, or to contact the author of the corresponding post directly.

Software contained in the TPP

Probability Assignment and Validation

PeptideProphet: Statistical validation of PSMs using search engine results.

iProphet: Distinct peptide sequence validation, using PeptideProphet results; can also combine the results of multiple search engines.

ProteinProphet: Protein identification and validation, using PeptideProphet OR iProphet results.

Mayu: Decoy-estimated FDRs (false discovery rate) for PeptideProphet results.

Protein Quantification

XPRESS: Calculation of relative abundances of peptides and proteins from isotopically labeled MS/MS samples.

ASAPRatio: Automated Statistical Analysis on Protein Ratio; an alternative to XPRESS.

Libra: Quantification of isobarically-labeled samples (e.g. iTraq, TMT, etc) for any number of channels

Graphical User Interface (GUI)

Petunia: Petunia is the name of the TPP's web-based GUI, which presents the tools in an organized and logical manner for those who do not wish to use the command-line.

Spectral Library Building and Searching

SpectraST: Searches spectral libraries (including publicly available ones from NIST and GPM) to identify peptide MS/MS spectra. Builds spectral libraries from sequence search results.

Protein ID Curation

Out2Summary - converter of SEQUEST and TurboSEQUEST *.out files into a single HTML-SUMMARY file ready for use with INTERACT

Pep3D: Viewer for LC-MS and LC-MS/MS results.

Input Processing: mzXML Tools

readmzXML: mzXML parser based on RAMP

MzXML2Search: Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files

mzStar: SCIEX/ABI Analyst format to mzXML converter

ReAdW: ThermoFinnigan Xcalibur format to mzXML converter

MZIdentML: Handling MZIdentml

RAMP: mzXML data parser

Input Processing: Search-Engine to pepXML converters

Database Search Tools

Working with supported search engines

The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, Comet, SpectraST, MSGF+, Inspect, MyriMatch, and Phenyx. Please see the supported search engines page for more information.

Example Data Analysis

TPP and Related Software Tools

This page describes the (sometimes confusing!) relationship between the many software projects that integrate with the TPP, either as compatible search engines, or as projects that repackage and redistribute the TPP itself.

Additional help


Frequently Asked Questions


subscriptions highly recommended for SPC Tools users


spctools-discuss discussion group: very active, daily discussions ranging from installation to data processing. All users, new and experienced, encouraged to participate.


spctools-announce discussion group: infrequent, important notifications of updates to our software

TPP Demo and Tutorial

Try or end-to-end analysis of Orbitrap SILAC data in our TPP Tutorial.

Developer Documentation


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