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Briefings in Functional Genomics 2009 8(2):114-125; doi:10.1093/bfgp/elp008
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© The Author 2009. Published by Oxford University Press. For permissions, please email: journals.permissions@oxfordjournals.org

This article appears in the following Briefings in Functional Genomics and Proteomics issue: Special Issue: Target Quantitative Proteomics: The Next Logical Step in Proteomics [View the issue table of contents]

Special Issue Papers

Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics

Kelli G. Kline, Greg L. Finney and Christine C. Wu

Corresponding author. Christine C. Wu, Department of Pharmacology, University of Colorado School of Medicine, Fitzsimons RC1 South L18-6117, PO Box 6511, Mail Stop 8303, Aurora, CO 80045, USA. Tel: +1 303 724 3351; Fax: +1 303 724 3663; E-mail: christine.wu{at}ucdenver.edu

The ultimate goal of most shotgun proteomic pipelines is the discovery of novel biomarkers to direct the development of quantitative diagnostics for the detection and treatment of disease. Differential comparisons of biological samples identify candidate peptides that can serve as proxys of candidate proteins. While these discovery approaches are robust and fairly comprehensive, they have relatively low throughput. When merged with targeted mass spectrometry, this pipeline can fuel hypothesis-driven studies and the development of novel diagnostics and therapeutics.

Keywords: quantitative shotgun proteomics, biomarker discovery, targeted mass spectrometry, human tissue


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