Software:TPP
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Revision as of 23:06, 10 April 2007 Jtasman (Talk | contribs) (adding download information) Next diff → |
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| [[image:TPP_overview.gif]] | [[image:TPP_overview.gif]] | ||
| - | Software contained in the TPP: | ||
| + | ==Getting the software== | ||
| - | ==Probability Assignment and Validation== | + | ===[[TPP:Windows Cygwin Installation|Installing on a Windows System]]=== |
| + | |||
| + | ===Source code (For Linux systems)=== | ||
| + | The latest source code package can be found [http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912 here], on the Sashimi project site on SourceForge. | ||
| + | |||
| + | ===[[TPP:Installing on Mac OSX|Mac OSX Installation guide]]=== | ||
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| + | <!-- <P>Download source from local site: <a href="./software/TPP_v2.9.7_GALE.zip">TPP_v2.9.7_GALE.zip</a></P> --> | ||
| + | <!-- <P>Download cygwin binaries: <a href="windows.php">Windows installation</a></P> --> | ||
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| + | |||
| + | <!-- <P>Download source from Web: <a href="http://sourceforge.net/project/showfiles.php?group_id=69281">Sourceforge Page</a><br> --> | ||
| + | <!-- <em>Note: On the web you might find a newer version of this software.</em></P> --> | ||
| + | |||
| + | |||
| + | ==Software contained in the TPP== | ||
| + | |||
| + | |||
| + | ===Probability Assignment and Validation=== | ||
| [[Software:PeptideProphet|PeptideProphet]]: Statistical validation of spectra-to-peptide sequence, using search engine results. | [[Software:PeptideProphet|PeptideProphet]]: Statistical validation of spectra-to-peptide sequence, using search engine results. | ||
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| [[Software:ProteinProphet|ProteinProphet]]: Protein identification and validation, using [[Software:PeptideProphet|PeptideProphet]] results. | [[Software:ProteinProphet|ProteinProphet]]: Protein identification and validation, using [[Software:PeptideProphet|PeptideProphet]] results. | ||
| - | ==Protein Quantification== | + | ===Protein Quantification=== |
| [[Software:XPRESS|XPRESS]]: Calculation of relative abundance of proteins from MS/MS data. | [[Software:XPRESS|XPRESS]]: Calculation of relative abundance of proteins from MS/MS data. | ||
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| [[Software:Libra|Libra]]: Four channel quantification software. | [[Software:Libra|Libra]]: Four channel quantification software. | ||
| - | ==Graphical User Interface (GUI)== | + | ===Graphical User Interface (GUI)=== |
| [[Software:Petunia|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. | [[Software:Petunia|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== | + | ===Protein ID Curation=== |
| Out2Summary - converter of SEQUEST and TurboSEQUEST *.out files into a single HTML-SUMMARY file ready for use with INTERACT | Out2Summary - converter of SEQUEST and TurboSEQUEST *.out files into a single HTML-SUMMARY file ready for use with INTERACT | ||
| [[Software:Pep3D|Pep3D]]: Viewer for LC-MS and LC-MS/MS results. | [[Software:Pep3D|Pep3D]]: Viewer for LC-MS and LC-MS/MS results. | ||
| - | ==Input Processing: mzXML Tools== | + | ===Input Processing: mzXML Tools=== |
| readmzXML: mzXML parser based on RAMP | readmzXML: mzXML parser based on RAMP | ||
Revision as of 23:06, 10 April 2007
The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
Contents |
Getting the software
Installing on a Windows System
Source code (For Linux systems)
The latest source code package can be found here, on the Sashimi project site on SourceForge.
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
