A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS

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Abstract

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 article are available at http://proteomics.fhcrc.org/.

Matthew Bellew, Marc Coram, Matthew Fitzgibbon, Mark Igra, Tim Randolph, Pei Wang, Damon May, Jimmy Eng, Ruihua Fang, ChenWei Lin, Jinzhi Chen, David Goodlett, Jeffrey Whiteaker, Amanda Paulovich and Martin McIntosh. 2006. A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. Bioinformatics 22(15):1902-1909.

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