Software:TPP

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Revision as of 22:54, 14 October 2014

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

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

Latest download (4.7.1)

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.

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.

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.

Using the TPP web interface ("Petunia")

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

What's New

The TPP:Recent Updates page describes updates to the software.

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

Frequently Asked Questions

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.

 ===Probability Assignment and Validation===
-[[Software:PeptideProphet|PeptideProphet]]: Statistical validation of spectra-to-peptide sequence, using search engine results.
+[[Software:PeptideProphet|PeptideProphet]]: Statistical validation of PSMs using search engine results.
-[[Software:ProteinProphet|ProteinProphet]]: Protein identification and validation, using [[Software:PeptideProphet|PeptideProphet]] results.
+[[Software:iProphet|iProphet]]: Distinct peptide sequence validation, using [[Software:PeptideProphet|PeptideProphet]] results; can also combine the results of multiple search engines.
+[[Software:ProteinProphet|ProteinProphet]]: Protein identification and validation, using [[Software:PeptideProphet|PeptideProphet]] OR [[Software:iProphet|iProphet]] results.
 [[Software:Mayu|Mayu]]: Decoy-estimated FDRs (false discovery rate) for [[Software:PeptideProphet|PeptideProphet]] results.