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Seattle Proteome Center (SPC) - Proteomics Tools
NHLBI Proteomics Center at the Institute for Systems Biology

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PROTEOMICS TOOLS



The Trans-Proteomic Pipeline (TPP) (Windows installation: run the TPP_Cygwin_Setup.exe program) includes all of the steps of the ISB MS/MS analysis pipeline, after the database search. Most users will only need to download the TPP distrubtion.

The individual tools that make up the TPP, as well as a few which are not included in the TPP distrubution, are categorized below.

Please also see the SPC Tools Wiki for more information, including download information.
  • Input Processing / Data Handling
    • mzXML - standard format for mass-spectrometry data
    • ReAdW - ThermoFinnigan Xcalibur format to mzXML converter
    • MassWolf - Micromass MassLynx format to mzXML converter
    • mzStar - SCIEX/ABI Analyst format to mzXML converter
    • mzBruker - Bruker format to mzXML converter
    • RAP, JRAP, RAMP - mzXML data parsers
    • validateXML - mzXML validation script
    • MsXML2Other - mzXML to SEQUEST dta, MASCOT generic and Micromass pkl converter
    • mzXMLViewer - viewer for displaying mzXML data
    • InsilicosViewer - viewer for displaying mzXML data
    • readmzXML - mzXML parser based on RAMP
  • Probability Assignment and Validation
    • PeptideProphetTM - validation of peptide identifications made by tandem mass spectrometry (MS/MS) and database searching; probabilities are assigned to the peptide identifications made by programs like SEQUEST or MASCOT
    • ProteinProphetTM - statistical model for validation of peptide identifications at the protein level
  • Protein Quantification
    • XPRESS - software to calculate the relative abundance of proteins in the sample
    • ASAPRatio - Automated Statistical Analysis on Protein Ratio
    • Libra - Four channel quantification software
  • Protein ID Curation
    • QualScore-- analyze unassigned but hig quality spectra.
    • PepXMLViewer - peptide dataset interaction
    • Pep3D - viewer for LC-MS and LC-MS/MS results
    • Out2Summary - converter of SEQUEST and TurboSEQUEST *.out files for TPP processing into a single HTML-SUMMARY file ready for use with INTERACT
  • Protein Crosslinking
  • Miscellaneous
  • LC-MS Analysis
    • SpecArray - tool for analyzing and comparing LC-MS runs
    • SuperHirn - label-free quantitative analysis.
    • MSAnalyzer - alternate tool for MS Level 1 analysis.
  • Interpretation
    • SBEAMS - Systems Biology Experiment Analysis Management System
    • Cytoscape - platform for visualizing and integrating molecular interaction networks
    • Prequips: Prequips is an interactive software environment for integration, visualization and analysis of LC-MS/MS data.
 

NHLBI Proteomics Center @ ISB