The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
<imagemap> image:TPP.jpg| rect 940 142 760 88 [] rect 940 203 760 153 [] rect 940 273 760 219 [] rect 1431 173 1250 88 [] rect 454 176 273 134 [] rect 454 128 273 88 [] rect 1185 273 1010 88 [] rect 700 144 515 88 [] rect 700 207 515 152 [] rect 264 333 50 300 [] rect 1058 333 425 300 [] rect 1377 333 1168 300 [] rect 1433 270 1250 185 [] desc none </imagemap>
Authors and Contributors
Getting the software
For support both during and after installation, you are strongly encouraged to consult the SPC Tools newsgroups:
- The spctools-discuss discussion group provides active community support and discussion for the tools.
- Important information about new releases and software updates can be found on the spctools-announce discussion group. You are highly encouraged to subscibe to this low-volume list.
Installing on a Windows System
Source code Installation (For Linux systems)
The latest source code package can be found here, on the Sashimi project site on SourceForge. Details on how to build 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.
- TPP:Building Windows-native binaries with Mingw
- TPP:Building Windows-native binaries with Visual Studio 2005
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.
- Mac OSX Installation guide by Ulrich auf dem Keller
- Installing TPP 4.6.2 on Mountain Lion Mac OSX by Bosco Ho
Software contained in the TPP
Probability Assignment and Validation
PeptideProphet: Statistical validation of PSMs using search engine results.
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
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
- X!Tandem: Open source peptide search engine from GPM
- Comet: Open source peptide search engine from Comet-MS
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
- Example Data Analysis
- Try our TPP Tutorial
- You can also see the older TPP Tutorial v2 and TPP Tutorial v1
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.
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
- Boost CPP libraries
- Debugging:Understanding XSL-Generating Code in Perl
- Debugging:Working with boost::shared ptr