Software:Overview

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Revision as of 22:09, 9 April 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

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Trans-Proteomic Pipeline

Please see the TPP page for descriptions of the pipeline and these components.

This software distribution integrates the following programs:

  • Petunia (TPP GUI)
  • PeptideProphet
  • ProteinProphet
  • XPRESS
  • ASAPRatio
  • Libra
  • Pep3D
  • Out2Summary
  • MsXML2Other
  • readmzXML
  • mzStar
  • ReAdW
  • Qualscore
  • RAMP


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LC-MS Analysis

SpecArray: tool for analyzing and comparing LC-MS runs

MSAnalyzer: alternate tool for MS Level 1 analysis.

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Interpretation

SBEAMS: Systems Biology Experiment Analysis Management System

Cytoscape: platform for visualizing and integrating molecular interaction networks

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Protein Crosslinking

XLink: XLink suite

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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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