Abstract
Rat brain proteomics is progressing gradually from gel-based approaches to gel-free systems and the emerging technique of MALDI imaging is making its mark on direct analysis of proteins in the brain sections. In this protocol chapter, we provide the details on the sample preparation methods for brain proteins analysis by mass spectrometry. Sample preparation methods include first grinding the brain and/or its regions in liquid nitrogen, followed by extracting proteins efficiently with various extraction buffers. The two protocols described here, are the modified TCA/acetone extraction method and extraction using Tris-buffered saline with addition of Tween 20. The soluble proteins obtained from the powdered brain samples can be directly analyzed after digestion with trypsin by gel-free approach to enhance the proteome coverage. Finally, we present a detailed protocol for protein identification in brain sections using the emerging technology of MALDI imaging.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aebersold, R., and Mann, M. (2003). Mass spectrometry-based proteomics. Nature 422, 198–207.
Agrawal, G.K., and Rakwal, R. (eds.) (2008). Plant Proteomics: Technologies, Strategies, and Applications (Hoboken, NJ, Wiley).
Chaurand, P., et al. (2008). Imaging mass spectrometry of intact proteins from alcohol-preserved tissue specimens: Bypassing formalin fixation. J Proteome Res 7, 3543–3555.
Cox, J., and Mann, M. (2007). Is proteomics the new genomics? Cell 130, 395–398.
Dwinell, M.R., et al. (2009). The Rat Genome Database 2009: Variation, ontologies and pathways. Nucleic Acids Res 37, D744–D749.
Fountoulakis, M. (2004). Application of proteomics technologies in the investigation of the brain. Mass Spectrom Rev 23, 231–258.
Fountoulakis, M., and Kossida, S. (2006). Proteomics-driven progress in neurodegeneration research. Electrophoresis 27, 1556–1573.
Fountoulakis, M., Tsangaris, G.T., Maris, A., and Lubec, G. (2005). The rat brain hippocampus proteome. J Chrom B 819, 115–129.
Franck, J., Arafah, K., Barnes, A., Wisztorski, M., Salzet, M., and Fournier, I. (2009a). Improving tissue preparation for matrix-assisted laser desorption ionization mass spectrometry imaging. Part 1: using microspotting. Anal Chem 81, 8193–8202.
Franck, J., Ayed, E., Wisztorski, M., Salzet, M., and Fournier, I. (2009b). On Tissue N-terminal peptide derivatizations for enhancing protein identification in MALDI-MSI strategies. Anal Chem 81, 8305–8317.
Garbis, S., Lubec, G., and Fountoulakis, M. (2005). Limitations of current proteomics technologies. J Chromatogr A 1077, 1–18.
Gibbs, R.A., et al. (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521.
Glowinski, J., and Iversen, L.L. (1966). Regional studies of catecholamines in the rat brain. I. The disposition of [3H]norepinephrine, [3H]dopamine and [3H]dopa in various regions of the brain. J Neurochem 13, 655–669.
Hirano, M., et al. (2006). New protein extraction/solubilization protocol for gel-based proteomics of rat (female) whole brain and brain regions for investigating central nervous system disorders. Mol Cells 22, 119–125.
Hirano, M., et al. (2008). Proteomics- and transcriptomics-based screening of differentially expressed proteins and genes in brain of Wig rat: A model for attention deficit hyperactivity disorder (ADHD) research. J Proteome Res 7, 2471–2489.
Hirano, M., et al. (2007). Gel-based proteomics of unilateral irradiated striatum after gamma knife surgery. J Proteome Res 6, 2656–2668.
Kang, D., et al. (2005). Dual-purpose sample trap for on-line strong cation-exchange chromatography/reversed-phase liquid chromatography/tandem mass spectrometry for shotgun proteomics. Application to the human Jurkat T-cell proteome. J Chromatogr A 1070, 193–200.
Kim, S.-Y., et al. (2005). Proteomic analysis of phosphotyrosyl proteins in morphine-dependent rat brains. Mol Brain Res 133, 58–70.
Klose, J. (2009). From 2-D electrophoresis to proteomics. Electrophoresis 30, S142–S149.
Koller, A., Washburn, M.P., et al. (2002). Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci USA 99, 11969–11974
Lemaire, R., Tabet, J.C., Ducoroy, P., Hendra, J.B., Salzet, M., and Fournier, I. (2006a). Solid ionic matrixes for direct tissue analysis and MALDI imaging. Anal Chem 78, 809–819.
Lemaire, R., Wisztorski, M., Desmons, A., Tabet, J.C., Day, R., Salzet, M., and Fournier, I. (2006b). MALDI-MS direct tissue analysis of proteins: Improving signal sensitivity using organic treatments. Anal Chem 78, 7145–7153.
Masuo, Y., et al. (2009). Omic analyses unravels global molecular changes in the brain and liver of a rat model for chronic Sake (Japanese alcoholic beverage) intake. Electrophoresis 30, 1259–1275.
Mathy, G., and Sluse, F.E. (2008). Mitochondrial comparative proteomics: Strengths and pitfalls. Biochim Biophys Acta 1777, 1072–1077.
Mu, J., et al. (2008). Proteomic analysis of a rat model of depression. Expert Rev Proteomics 5, 315–320.
Paulson, L., et al. (2004). Comparative proteome analysis of thalamus in MK-801-treated rats. Proteomics 4, 819–825.
Sagvolden, T., et al. (2005). Rodent models of attention-deficit/hyperactivity disorder. Biol Psychiatry 57, 1239–1247.
Schmidt, M.V., et al. (2008). Chronic stress and individual vulnerability. Ann N Y Acad Sci 1148, 174–183.
Seo, H.S., Hirano, M., Shibato, J., Rakwal, R., Hwang, I.K., and Masuo, Y. (2008). Effects of coffee bean aroma on the rat brain stressed by sleep deprivation: A selected transcript- and 2D gel-based proteome analyses. J Agric Food Chem 56, 4665–4673.
Steinberg, T.H., et al. (2003). Global quantitative phosphoprotein analysis using multiplexed proteomics technology. Proteomics 3, 1128–1144.
Tafet, G.E., and Bernardini, R. (2003). Psychoneuroendocrinological links between chronic stress and depression. Prog Neuropsychopharmacol Biol Psychiatry 27, 893–903.
Washburn, M.P., Wolters, D., and Yates J.R. 3rd (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19, 242–247.
Wilkins, M.R., Sanchez, J.C., Gooley, A.A., Appel, R.D., Humphery-Smith, I., et al. (1995). Progress with proteome projects: Why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13, S19–S50.
Williams, K., et al. (2004). Recent advances in neuroproteomics and potential application to studies of drug addiction. Neuropharmacology 47, 148–166.
Wisztorski, M., Croix, D., Macagno, E., Fournier, I., and Salzet, M. (2008). Molecular MALDI imaging: An emerging technology for neuroscience studies. Dev Neurobiol 68, 845–858.
Yeom, M., Shim, I., Lee, H.-J., and Hahm, D.-H. (2005). Proteomic analysis of nicotine-associated protein expression in the striatum of repeated nicotine-treated rats. Biochem Biophys Res Commun 326, 321–328.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media B.V.
About this chapter
Cite this chapter
Masuo, Y. et al. (2011). Brain Proteomics: Sample Preparation Techniques for the Analysis of Rat Brain Samples Using Mass Spectrometry. In: Ivanov, A., Lazarev, A. (eds) Sample Preparation in Biological Mass Spectrometry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0828-0_11
Download citation
DOI: https://doi.org/10.1007/978-94-007-0828-0_11
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-0758-0
Online ISBN: 978-94-007-0828-0
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)