Software:Overview
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| The Seattle Proteome Center (SPC) at the ISB has produced many open-source proteomics tools, many of which are integrated into the [[Software:TPP|TPP]] project. | The Seattle Proteome Center (SPC) at the ISB has produced many open-source proteomics tools, many of which are integrated into the [[Software:TPP|TPP]] project. | ||
| - | ==Trans-Proteomic Pipeline== | + | ==The Trans-Proteomic Pipeline (TPP) Project== |
| '''Please see the [[Software:TPP|TPP page]] for descriptions of the pipeline and these components.''' | '''Please see the [[Software:TPP|TPP page]] for descriptions of the pipeline and these components.''' | ||
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| *Qualscore | *Qualscore | ||
| *RAMP | *RAMP | ||
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| ==LC-MS Analysis== | ==LC-MS Analysis== | ||
Revision as of 21:48, 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: in TPP tools
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
