Software:TPP
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| Software contained in the TPP: | Software contained in the TPP: | ||
| - | ==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)== | ||
| - | [[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. | ||
| ==Probability Assignment and Validation== | ==Probability Assignment and Validation== | ||
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| [[Software:Libra|Libra]]: Four channel quantification software. | [[Software:Libra|Libra]]: Four channel quantification software. | ||
| + | |||
| + | ==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. | ||
| ==Protein ID Curation== | ==Protein ID Curation== | ||
| Line 36: | Line 25: | ||
| [[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== | ||
| + | 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 | ||
Revision as of 22:41, 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 |
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
