Projects Publications Members Collaborators Go to CPAS


The Computational Proteomics Laboratory (CPL) at Fred Hutchinson Cancer Research Center (FHCRC) develops and uses computational approaches for protein and proteomics research. As Principal Investigator, Dr. Martin McIntosh leads the CPL's substantive research, which centers on serum proteomics for disease detection and classification. The CPL also collaborates with other researchers at the FHCRC and around the world on a variety of bioinformatics projects.

Software Platforms

msInspect - mass spectrometry In silico peptide characterization tool
msInspect

msInspect is a suite of software and algorithms for viewing and processing data from liquid chromatography-mass spectrometry (LC-MS) measurements. It is also a platform for proteomics application development. All of our tools built on the msInspect platform are free, cross-platform, and open source.

Qurate - A tool within the msInspect platform for visual curation and management of quantitative ratio data from isotopically labeled LC-MS/MS experiments.

Qurate

Published in the Journal of Proteome Research:

MRMer - A tool within the msInspect platform for evaluating MRM ion candidates and measuring product-ion quantities. Developed in partnership with Dr. Dan Martin, ISB.

MRMer

Published in Molecular and Cellular Proteomics:

msInspect/AMT - A full workflow within msInspect for creating Accurate Mass and Time (AMT) databases, matching LC-MS peptide features to them, and integrating the results with MS/MS search results.

msInspect/AMT Published in the Journal of Proteome Research:

CPAS - Computational Proteomics Analysis System
CPAS


CPAS is a suite of database and analysis tools, originally developed in the FHCRC CPL, that manages proteomics experimental workflows and integrates database search algorithms (X!Tandem, Mascot, and Sequest) and Institute for Systems Biology (ISB) data management tools.  CPAS is now distributed as part of the <a href="https://www.labkey.org">Labkey Server</a>, an open source project managed by the Labkey Software Foundation. The primary (but not sole) developers of Labkey are <a href="http://www.labkey.com">Labkey.com</a>, a consulting firm founded by former FHCRC employees.
Our software platforms make use of Institute for Systems Biology (ISB) tools available at the Sashimi site, the Global Proteome Machine's X! Tandem project, and the R statistical programming language.

More Software Tools

Some of our software tools are built into msInspect or CPAS while others are stand-alone tools. Below is a list of software tools with links to published manuscripts describing their use, supplementary material to the published work (when available), and access to the most current version of the software.
  • K-score Pluggable Scoring algorithm: A framework for incorporating novel scoring algorithms into X!Tandem that is compatible with PeptideProphet.
  • Retention time normalization algorithm: A method built into msInspect for normalizing peptide arrays from label-free LC-MS data.
  • PETAL: A method developed by Dr. Pei Wang and CPL for alignment across multiple LC-MS arrays.
  • Q3: A method built into msInspect for quantitative proteomics with LC-MS/MS and high resolution instrumentation that is compatible with acrylamide labeling.
  • Retention Time prediction: A method for predicting retention times in LC-MS/MS experiments and for normalizing retention times across experiments.
  • SASPECT: A method developed by Dr. Pei Wang and the Paulovich laboratory for predicting false discovery rates using spectral counts when comparing two groups of proteins.