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 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:

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

mzBruker

validateXML

mzXMLViewer

InsilicosViewer

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