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Briefings in Functional Genomics and Proteomics Advance Access published online on December 24, 2008
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/eln051
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© The Author 2008. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Challenges and strategies for targeted phosphorylation site identification and quantification using mass spectrometry analysis

Kevin Blackburn and Michael B. Goshe

Corresponding author. 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

Despite its importance, the ‘ultimate’ method to identify and quantify site-specific protein phosphorylation using mass spectrometry (MS) has yet to be established. This is as much a function of the dynamic range of instrumentation as it is the complexities surrounding the isolation and behavior of phosphopeptides. Phosphorylation site analysis using MS can be quite challenging when analyzing just one protein and quickly becomes a daunting task when attempting to perform proteome-wide measurements. Data-dependent tandem MS-based methods which are useful for the discovery and characterization of novel phosphorylation sites often lack the dynamic range and quantitative aspect required for studying the temporal phases of phosphorylation. While targeted methods such as multiple reaction monitoring do provide a highly specific and quantitative methodology for studying phosphorylation changes over time, they are not suited for initial discovery of previously unreported sites of phosphorylation. Data-independent acquisition represents a relatively new approach for simultaneous qualitative and quantitative sample analysis which holds promise for filling this technological gap.

Keywords: phosphorylation site stoichiometry, phosphorylation site identification, data-dependent acquisition, data-independent acquisition, multiple reaction monitoring, LC/MSE


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