Proteomic Analysis of Mouse Brain Microsomes: Identification and Bioinformatic Characterization of Endoplasmic Reticulum Proteins in the Mammalian Central Nervous System

Stanley M. Stevens, R. Scott Duncan, Peter Koulen, Laszlo Prokai

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

The endoplasmic reticulum (ER) is the main source for the storage and release of intracellular calcium in neurons and, thus, contributes to the functionality of a diverse set of pathways that control critical aspects of central nervous system function including but not limited to gene expression, neurotransmission, learning, and memory. ER-derived proteins obtained after subcellular fractionation of mouse brain homogenate were digested with trypsin and the corresponding peptides fractionated by strong cation exchange chromatography followed by LC-MS/MS analysis on a hybrid linear ion trap-Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. A comprehensive catalogue representing 1914 proteins was generated from this particular proteomic analysis using identification criteria that corresponded to a false positive identification rate of 0.4%. Various molecular functions and biological processes relevant to the ER were identified upon gene ontology (GO)-based analysis including pathways associated with molecular transport, protein trafficking and localization, and cell signaling. Comparison of the 2D-LC-MS/MS results with those obtained from shotgun LC-MS/MS analyses demonstrated that most molecular functions and biological processes were represented via GO analysis using either methodology. Results from this comparison as well as a focused investigation into components of calcium-mediated signaling in the mouse brain ER are also presented.

Original languageEnglish
Pages (from-to)1046-1054
Number of pages9
JournalJournal of Proteome Research
Volume7
Issue number3
DOIs
StatePublished - Mar 2008

Keywords

  • Brain microsomes
  • Calcium signaling
  • Endoplasmic
  • Fractionation, fourier transform ion cyclotron resonance mass spectrometry
  • Proteomics
  • Reticulum
  • Subcellular

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