Software:Overview
From SPCTools
The Seattle Proteome Center (SPC) at the ISB has produced many open-source proteomics tools, many of which are integrated into the TPP project.
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The Trans-Proteomic Pipeline (TPP) Project
Please see the TPP page for descriptions of the pipeline and these components and installation instructions.
The TPP 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
Again, please see he TPP page for descriptions of the pipeline and these components and installation instructions.
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
