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Molecular & Cellular Proteomics 6:283-293, 2007.
© 2007 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Qualitative and Quantitative Analyses of Protein Phosphorylation in Naive and Stimulated Mouse Synaptosomal Preparations^*,S

Richard P. Munton^,, Ry Tweedie-Cullen^,, Magdalena Livingstone-Zatchej^,, Franziska Weinandy, Marc Waidelich, Davide Longo, Peter Gehrig^¶, Frank Potthast^¶, Dorothea Rutishauser^¶, Bertran Gerrits^¶, Christian Panse^¶, Ralph Schlapbach^¶ and Isabelle M. Mansuy^,||

From the Brain Research Institute, Medical Faculty of the University of Zürich and Department of Biology of the Swiss Federal Institute of Technology and ^¶ Functional Genomics Center Zürich, University of Zürich and Swiss Federal Institute of Technology, CH-8057 Zürich, Switzerland

Activity-dependent protein phosphorylation is a highly dynamic yet tightly regulated process essential for cellular signaling. Although recognized as critical for neuronal functions, the extent and stoichiometry of phosphorylation in brain cells remain undetermined. In this study, we resolved activity-dependent changes in phosphorylation stoichiometry at specific sites in distinct subcellular compartments of brain cells. Following highly sensitive phosphopeptide enrichment using immobilized metal affinity chromatography and mass spectrometry, we isolated and identified 974 unique phosphorylation sites on 499 proteins, many of which are novel. To further explore the significance of specific phosphorylation sites, we used isobaric peptide labels and determined the absolute quantity of both phosphorylated and non-phosphorylated peptides of candidate phosphoproteins and estimated phosphorylation stoichiometry. The analyses of phosphorylation dynamics using differentially stimulated synaptic terminal preparations revealed activity-dependent changes in phosphorylation stoichiometry of target proteins. Using this method, we were able to differentiate between distinct isoforms of Ca²⁺/calmodulin-dependent protein kinase (CaMKII) and identify a novel activity-regulated phosphorylation site on the glutamate receptor subunit GluR1. Together these data illustrate that mass spectrometry-based methods can be used to determine activity-dependent changes in phosphorylation stoichiometry on candidate phosphopeptides following large scale phosphoproteome analysis of brain tissue.

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