Software:TPP

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==Working with supported search engines== ==Working with supported search engines==
-The TPP currently supports Sequest, Mascot, X!Tandem, and Phenyx. Please see the [[TPP:Supported Search Engines|supported search engines]] page for more information.+The TPP currently supports Sequest, Mascot, ProbID, X!Tandem, and Phenyx. Please see the [[TPP:Supported Search Engines|supported search engines]] page for more information.
==Additional help== ==Additional help==

Revision as of 23:10, 6 July 2007

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

image:TPP_overview.gif


Contents

Getting the software

Support Note

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

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.

Installing on Ubuntu

These community-contributed notes are a guide to installing on the Ubuntu distribution but should be similar to other linux systems.

Mac OSX Installation guide

Software contained in the TPP

Probability Assignment and Validation

PeptideProphet: Statistical validation of spectra-to-peptide sequence, using search engine results.

ProteinProphet: Protein identification and validation, using PeptideProphet results.

Protein Quantification

XPRESS: Calculation of relative abundance of proteins from MS/MS data.

ASAPRatio: Automated Statistical Analysis on Protein Ratio.

Libra: Four channel quantification software.

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.

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

MsXML2Other: mzXML to SEQUEST dta, MASCOT generic and Micromass pkl converter

mzStar: SCIEX/ABI Analyst format to mzXML converter

ReAdW: ThermoFinnigan Xcalibur format to mzXML converter

RAMP: mzXML data parser

Input Processing: Search-Engine to pepXML converters

Working with supported search engines

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

Additional help

Frequently Asked Questions

spctools-discuss discussion group

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