Software:TPP

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* Important information about new releases and software updates can be found on the [http://groups.google.com/group/spctools-announce spctools-announce discussion group]. You are '''highly encouraged''' to subscibe to this low-volume list. * Important information about new releases and software updates can be found on the [http://groups.google.com/group/spctools-announce spctools-announce discussion group]. You are '''highly encouraged''' to subscibe to this low-volume list.
-===[[TPP:Windows Cygwin Installation|Installing on a Windows System]]===+===Installing on a Windows System===
 +[[http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 Click here for the latest download]]
===Source code Installation (For Linux systems)=== ===Source code Installation (For Linux systems)===

Revision as of 17:32, 24 October 2008

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 strongly encouraged to consult the SPC Tools newsgroups:

Installing on a Windows System

[Click here for the latest download]

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.

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

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.

Example Data Analysis

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 Tutorial

TPP Tutorial

Developer Documentation

Links

Personal tools