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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 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.

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

msBID: alternate tool for MS Level 1 analysis.

Pep3D: Visualization tool for viewing MS and MS/MS runs; integrated into the TPP.

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

Protein Crosslinking


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





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