Software:TPP

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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

Additional help

Frequently Asked Questions

spctools-discuss discussion group

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