Quantitative proteomic profiling of membrane proteins

Brain Res. 2007 Jan 4; [Epub ahead of print]

Quantitative proteomic profiling of membrane proteins from the mouse brain cortex, hippocampus, and cerebellum using the HysTag reagent: Mapping of neurotransmitter receptors and ion channels

Jesper V. Olsen^a,b, Peter Aa. Nielsen^c,1, Jens R. Andersen^c, Matthias Mann^a,b,*, Jacek R. Wiśniewski^b,c,*

^aCenter for Experimental BioInformatics (CEBI), University of Southern Denmark, Denmark
^bMax-Planck Institute for Biochemistry, 82152 Martinsried, Germany
^cMDS Inc. Denmark, 5230 Odense M, Denmark

Analysis of the brain proteome and studying brain diseases through clinical biopsies and animal disease models require methods of quantitative proteomics that are sensitive and allow identification and quantification of low abundant membrane proteins from minute amount of tissue. Taking advantage of recently developed methods for isolation of membrane proteins from 10–20 mg brain tissue [Nielsen, P.Aa., Olsen, J.V., Podtelejnokov, A.V., Andersen, J.R., Mann, M., Wiśniewski, J.R., 2005. Proteomic mapping of brain plasma membrane proteins. Mol. Cell. Proteomics 4, 402–408] and the HysTag-quantification method [Olsen, J.V., Andersen, J.R., Nielsen, P.Aa., Nielsen, M.L., Figeys, D., Mann, M., Wiśniewski, J.R., 2004. HysTag—A novel proteomic qualification tool applied to differential analysis of membrane proteins from distinct areas of mouse brain. Mol. Cell. Proteomics 3, 82–92] we performed quantitative proteomic analysis of three functionally distinct compartments of mouse brain: cortex, hippocampus, and cerebellum. In total, 976 unique peptides corresponding to 555 unique proteins were quantified. Up to 20-fold differences in the levels of some proteins between brain areas were measured. For many quantified proteins – as for glutamate receptors, calcium channel subunits, and ATP-ases – an excellent correlation between our proteomic data and previously published mRNA expression levels or intensity of immunostaining was found. Our results clearly demonstrate differences in levels of membrane proteins mapped in distinct brain compartments and offer a technology that allows in depth study of brain membrane proteomes, such as mouse models of neurological diseases.

^* Corresponding authors. Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, AmKlopferspitz 18, D-82152 Martinsried, Germany. Fax: +49 89 8578 2219. E-mail addresses: mmann@biochem.mpg.de (M. Mann), jwisniew@biochem.mpg.de (J.R. Wiśniewski). Abbreviations: LC, liquid chromatography; MS, mass spectrometry; MS/MS, tandem mass spectrometry; PM, plasma membrane; 2DE, two dimensional electrophoresis; MALDI TOF, matrix assisted laser desorption ionization—time of flight; LTQ, linear quadrupole ion trap; TOF, time of flight; FT, Fourier transform; FTICR, Fourier transform ion cyclotron resonance

1 Current address: Proxeon Biosystems, 5230 Odense M, Denmark.

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