The Seattle Proteome Center (SPC) at the ISB has produced many open-source proteomics tools, many of which are integrated into the TPP project.
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, SpectraST, Out2Summary, MzXML2Search, MsXML2Other, readmzXML, mzStar ReAdW, QualScore, RAMP, Out2XML, Mascot2XML, Tandem2XML
Again, please see the TPP page for descriptions of the pipeline and these components and installation instructions.
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).
SpecArray: tool for analyzing and comparing LC-MS runs
msBID: alternate tool for MS Level 1 analysis.
QualScore: reevaluating unassigned high-quality unassigned spectra.
SuperHirn: software for quantitative analysis of LC-MS data by a combined MS1 and MS2 approach
MS-MS Spectral Assignment
ProbID: open-source search engine
SWATH (DIA) anlaysis tools
SWATHProphet: A tool for statistical analysis of SWATH data and discovery of modifications
SBEAMS: Systems Biology Experiment Analysis Management System
Cytoscape: platform for visualizing and integrating molecular interaction networks
Firegoose, Gaggle, and PIPE: a suite of tools for analysis and visualization of biological data
XLink: XLink suite
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