Bioinformatics Advance Access published online on June 9, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl276
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1 LabKey Software, Seattle 98109, USA
* To whom correspondence should be addressed.
Motivation: Comparing two or more complex protein mixtures using liquid chromatography mass spectrometry (LC-MS) requires multiple analysis steps to locate and quantitate natural peptides within a single experiment and to align and normalize findings across multiple experiments. Results: We describe msInspect, an open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental measurements. The platform integrates novel algorithms for detecting signatures of natural peptides within a single LC-MS measurement and combines multiple experimental measurements into a peptide array, which may then be mined using analysis tools traditionally applied to genomic array analysis. The platform supports quantitation by both label-free and isotopic labeling approaches. The software implementation has been designed so that many key components may be easily replaced, making it useful as a workbench for integrating other novel algorithms developed by a growing research community. Availability: The msInspect software is distributed freely under an Apache 2.0 license. The software as well as a Zip file with all peptide feature files and scripts needed to generate the tables and figures in this paper are available at http://proteomics.fhcrc.org/. Supplementary Information: Supplementary materials are available at http://proteomics.fhcrc.org/CPAS (select "Published Experiments" from the list of Projects and then "msInspect Paper"). Associate Editor: Martin Bishop
Received March 6, 2006
Revised May 26, 2006
Accepted May 29, 2006
Article
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
Matthew Bellew 1 
,
Marc Coram 2 ,
Matthew Fitzgibbon 2 ,
Mark Igra 3 ,
Tim Randolph 2 ,
Pei Wang 2 ,
Damon May 2,
Jimmy Eng 2,
Ruihua Fang 2,
ChenWei Lin 2,
Jinzhi Chen 4,
David Goodlett 5,
Jeffrey Whiteaker 2,
Amanda Paulovich 2,
and
Martin McIntosh 2 *
2 Fred Hutchinson Cancer Research Center, Seattle 98109, USA
3 LabKey Software, Seattle 98109, USA; Fred Hutchinson Cancer Research Center, Seattle 98109, USA
4 Fred Hutchinson Cancer Research Center, Seattle 98109, USA; University of Washington, Seattle 98195, USA
5 University of Washington, Seattle 98195, USA
Martin McIntosh, E-mail: mmcintos{at}fhcrc.org
Abstract Authors listed alphabetically
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