Software:Overview
From SPCTools
| Revision as of 21:49, 10 April 2007 Jtasman (Talk | contribs) (→LC-MS Analysis) ← Previous diff |
Revision as of 22:21, 10 April 2007 Jtasman (Talk | contribs) (→The Trans-Proteomic Pipeline (TPP) Project) Next diff → |
||
| Line 7: | Line 7: | ||
| This software distribution integrates the following programs: | This software distribution integrates the following programs: | ||
| - | *Petunia (TPP GUI) | + | *[[Software:Petunia|Petunia (TPP GUI)]] |
| - | *PeptideProphet | + | *[[Software:PeptideProphet|PeptideProphet]] |
| - | *ProteinProphet | + | *[[Software:ProteinProphet|ProteinProphet]] |
| - | *XPRESS | + | *[[Software:XPRESS|XPRESS]] |
| - | *ASAPRatio | + | *[[Software:ASAPRatio|ASAPRatio]] |
| - | *Libra | + | *[[Software:Libra|Libra]] |
| - | *Pep3D | + | *[[Software:Pep3D|Pep3D]] |
| - | *Out2Summary | + | *[[Software:Out2Summary|Out2Summary]] |
| - | *MsXML2Other | + | *[[Software:MsXML2Other|MsXML2Other]] |
| - | *readmzXML | + | *[[Software:readmzXML|readmzXML]] |
| - | *mzStar | + | *[[Software:mzStar|mzStar]] |
| - | *ReAdW | + | *[[Software:ReAdW|ReAdW]] |
| - | *Qualscore | + | *[[Software:Qualscore|Qualscore]] |
| - | *RAMP | + | *[[Software:RAMP|RAMP]] |
| ==LC-MS Analysis== | ==LC-MS Analysis== | ||
Revision as of 22:21, 10 April 2007
The Seattle Proteome Center (SPC) at the ISB has produced many open-source proteomics tools, many of which are integrated into the TPP project.
Contents |
The Trans-Proteomic Pipeline (TPP) Project
Please see the TPP page for descriptions of the pipeline and these components.
This software distribution integrates the following programs:
- Petunia (TPP GUI)
- PeptideProphet
- ProteinProphet
- XPRESS
- ASAPRatio
- Libra
- Pep3D
- Out2Summary
- MsXML2Other
- readmzXML
- mzStar
- ReAdW
- Qualscore
- RAMP
LC-MS Analysis
SpecArray: tool for analyzing and comparing LC-MS runs
MSAnalyzer: alternate tool for MS Level 1 analysis.
Pep3D: Visualization tool for viewing MS and MS/MS runs; integrated into the TPP.
Interpretation
SBEAMS: Systems Biology Experiment Analysis Management System
Cytoscape: platform for visualizing and integrating molecular interaction networks
Protein Crosslinking
XLink: XLink suite
Miscellaneous
SPE: SEQUEST Parameter Editor tool
SubsetDB: tools for handling FASTA formatted databases
PeptideSieve: A tool for predicting proteotypic peptides
INTERACT - large dataset curation
CGIs - a bundle of useful CGI scripts
massWolf
mzBruker
validateXML
mzXMLViewer
InsilicosViewer
