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Briefings in Functional Genomics and Proteomics Advance Access originally published online on February 7, 2006
Briefings in Functional Genomics and Proteomics 2006 4(4):363-376; doi:10.1093/bfgp/eli007
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© The Author 2006. Published by Oxford University Press. All rights reserved. For permissions please email: journals.permissions@oxfordjournals.org

Technique Review

Characterizing phosphoproteins and phosphoproteomes using mass spectrometry

Michael B. Goshe

Dr Michael B. Goshe, Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Campus Box 7622, Raleigh, NC 27695-7622, USA. Tel: +1 919 513 7740; Fax: +1 919 515 2047; E-mail: michael_goshe{at}ncsu.edu

The reversible phosphorylation of proteins plays a major role in many vital cellular processes by modulating protein function and transmitting signals within cellular pathways and networks. Because phosphorylation is dynamic and the sites of modification cannot be predicted by an organism's genome, proteomic measurements are required to identify sites of and changes in the phosphorylation state of proteins. The low stoichiometry of phosphorylation sites that accompany the multifarious nature of protein phosphorylation in biological systems continues to challenge the dynamic range of present mass spectrometry (MS) technologies and proteomic measurements, despite the preponderance of research and analytical methods devoted to this area. This review addresses some of the strategies and limitations involving the use of MS to map and quantify changes in protein phosphorylation sites for samples that range from a single protein to an entire proteome, and presents several compelling reasons as to why comprehensive phosphorylation site analysis has proven to be so elusive without a hypothesis-driven experimental approach to elicit more meaningful and confident results.

Keywords: phosphoprotein, phosphoproteomics, proteomics, liquid chromatography, mass spectrometry, affinity labeling, stable isotope coding, quantification, quantitation


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