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Proteomic Standards Guidelines


(To navigate you can click on the chart below)


The Trans-Proteomic Pipeline (TPP) 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.

Download the TPP Installer for Windows

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 see the SPC Tools Wiki for more information, including download information.
  • Input Processing / Data Handling
    • mzXML - standard format for mass-spectrometry data
    • ReAdW - Thermo Xcalibur-to-mzXML converter
    • massWolf - Waters MassLynx raw-to-mzXML converter
    • mzWiff - ABI/MDS Sciex Analyst raw-to-mzXML converter
    • mzBruker - Bruker raw-to-mzXML converter
    • RAP, JRAP, RAMP - mzXML data parsers
    • validateXML - mzXML validation script
    • MzXML2Search - 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 high 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
    • Corra - Label free quantification and statistical analysis (Download VM image)
    • SpecArray - tool for analyzing and comparing LC-MS runs
    • SuperHirn - label-free quantitative analysis.
    • msBID - alternate tool for MS Level 1 analysis.
  • Interpretation
    • PIPE2 - Protein Information and Property Explorer2: Gaggle-like exploration of biological proteomic data within one webpage.
    • 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.
  • Under SRM Analysis
    • ATAQS: Computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. (Download VM image)
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