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

被引:207
作者
Bellew, Matthew
Coram, Marc
Fitzgibbon, Matthew
Igra, Mark
Randolph, Tim
Wang, Pei
May, Damon
Eng, Jimmy
Fang, Ruihua
Lin, ChenWei
Chen, Jinzhi
Goodlett, David
Whiteaker, Jeffrey
Paulovich, Amanda
McIntosh, Martin [1 ]
机构
[1] Fred Hutchinson Canc Res Ctr, Seattle, WA 98109 USA
[2] LabKey Software, Seattle, WA 98109 USA
[3] Univ Washington, Seattle, WA 98195 USA
关键词
D O I
10.1093/bioinformatics/btl276
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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/
引用
收藏
页码:1902 / 1909
页数:8
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