Software:TPP
From SPCTools
The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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Contents |
Authors and Contributors
See TPP:Authors and Contributors
Getting the software
Support Note
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
Detailed 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. These community-contributed notes are a guide to installing on the Ubuntu distribution but should be similar to other linux systems.
- TPP:Installing on Ubuntu 7.04
- TPP:Installing on Ubuntu 8.10
- TPP 4.2.1: Installing on Ubuntu 9.04
- TPP 4.3.1: Installing on Ubuntu 10.04
- TPP 4.5.2: Installing on Ubuntu 10.04.3
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
Mac OSX
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.
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
- Sequest results: Out2XML
- Mascot results: Mascot2XML
- Tandem results: Tandem2XML
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.
Additional help
FAQ
Newsgroups
subscriptions highly recommended for SPC Tools users
spctools-discuss
spctools-discuss discussion group: very active, daily discussions ranging from installation to data processing. All users, new and experienced, encouraged to participate.
spctools-announce
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
- Developer Documentation
- Boost CPP libraries
- Debugging:Understanding XSL-Generating Code in Perl
- Debugging:Working with boost::shared ptr
