Software:TPP

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	Software contained in the TPP:		Software contained in the TPP:
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		+	==Input Processing: mzXML Tools==
		+	readmzXML: mzXML parser based on RAMP
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		+	MsXML2Other: mzXML to SEQUEST dta, MASCOT generic and Micromass pkl converter
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		+	mzStar: SCIEX/ABI Analyst format to mzXML converter
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		+	ReAdW: ThermoFinnigan Xcalibur format to mzXML converter
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		+	RAMP: mzXML data parser
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	==Graphical User Interface (GUI)==		==Graphical User Interface (GUI)==

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Revision as of 22:12, 9 April 2007

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

Software contained in the TPP:

Contents 1 Input Processing: mzXML Tools 2 Graphical User Interface (GUI) 3 Probability Assignment and Validation 4 Protein Quantification 5 Protein ID Curation

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

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.

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.

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.