Software:Overview
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| ==The Trans-Proteomic Pipeline (TPP) Project== | ==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 and installation instructions.''' |
| This software distribution integrates the following programs: | This software distribution integrates the following programs: | ||
Revision as of 16:43, 10 May 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 and installation instructions.
This software distribution integrates the following programs:
- Petunia (TPP GUI)
- PeptideProphet
- ProteinProphet
- XPRESS
- ASAPRatio
- Libra
- Pep3D
- Out2Summary
- MzXML2Search
- MsXML2Other
- readmzXML
- mzStar
- ReAdW
- Qualscore
- RAMP
- Out2XML
- Mascot2XML
- Tandem2XML
Data Conversion
raw MS / MS2 to mzXML converters
Please see the mzXML page for info on ReAdW (Thermo), mzStar (ABI/MDS Sciex Analyst), massWolf (Waters MassLynx), and compassXport (Bruker).
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 (wolf.exe): Micromass MassLynx to mzXML converter
mzBruker: Bruker to mzXML converter
validateXML
mzXMLViewer
InsilicosViewer
