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Submitted on September 6, 2005
Dept. of Human Genetics, Emory University, Atlanta, GA 30322
Corresponding Author: jpeng{at}genetics.emory.edu
The postsynaptic density (PSD) of central excitatory synapses is essential for postsynaptic signaling and its components are heterogeneous among different neuronal subtypes and brain structures. We report here large-scale relative and absolute quantification of proteins in PSDs purified from adult rat forebrain and cerebellum. PSD protein profiles were determined using the cleavable isotope-coded affinity tag (ICAT) strategy and liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). A total of 296 proteins were identified and quantified, with 43 proteins exhibiting statistically significant abundance change between forebrain and cerebellum, indicating marked molecular heterogeneity of PSDs between different brain regions. Moreover, we utilized absolute quantification (AQUA) strategy, in which synthetic isotope-labeled peptides were used as internal standards, to measure the molar abundance of 32 key PSD proteins in forebrain and cerebellum. These data confirm the abundance of CaMKII and PSD-95 and reveal unexpected stoichiometric ratios between glutamate receptors, scaffold proteins as well as signaling molecules in the PSD. Our data also demonstrate that the AQUA method is well-suited for targeted quantitative proteomic analysis. Overall this study delineates crucial molecular difference between forebrain and cerebellar PSDs, and provides a quantitative framework for measuring the molecular stoichiometry of the PSD.
Revised on January 17, 2006
Accepted on February 28, 2006
Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum
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