Proteomic analysis of proteins expressing in regions of rat brain by a combination of SDS-PAGE with nano-liquid chromatography-quadrupole-time of flight tandem mass spectrometry

Tomoki Katagiri, Naoya Hatano, Masamune Aihara, Hiroo Kawano, Mariko Okamoto, Ying Liu, Tomonori Izumi, Tsuyoshi Maekawa, Shoji Nakamura, Tokuhiro Ishihara, Mutsunori Shirai, Yoichi Mizukami

Research output: Contribution to journalArticle

Abstract

Background: Most biological functions controlled by the brain and their related disorders are closely associated with activation in specific regions of the brain. Neuroproteomics has been applied to the analysis of whole brain, and the general pattern of protein expression in all regions has been elucidated. However, the comprehensive proteome of each brain region remains unclear.Results: In this study, we carried out comparative proteomics of six regions of the adult rat brain: thalamus, hippocampus, frontal cortex, parietal cortex, occipital cortex, and amygdala using semi-quantitative analysis by Mascot Score of the identified proteins. In order to identify efficiently the proteins that are present in the brain, the proteins were separated by a combination of SDS-PAGE on a C18 column-equipped nano-liquid chromatograph, and analyzed by quadrupole-time of flight-tandem-mass spectrometry. The proteomic data show 2,909 peptides in the rat brain, with more than 200 identified as region-abundant proteins by semi-quantitative analysis. The regions containing the identified proteins are membrane (20.0%), cytoplasm (19.5%), mitochondrion (17.1%), cytoskeleton (8.2%), nucleus (4.7%), extracellular region (3.3%), and other (18.0%). Of the identified proteins, the expressions of glial fibrillary acidic protein, GABA transporter 3, Septin 5, heat shock protein 90, synaptotagmin, heat shock protein 70, and pyruvate kinase were confirmed by immunoblotting. We examined the distributions in rat brain of GABA transporter 3, glial fibrillary acidic protein, and heat shock protein 70 by immunohistochemistry, and found that the proteins are localized around the regions observed by proteomic analysis and immunoblotting. IPA analysis indicates that pathways closely related to the biological functions of each region may be activated in rat brain.Conclusions: These observations indicate that proteomics in each region of adult rat brain may provide a novel way to elucidate biological actions associated with the activation of regions of the brain.

Original languageEnglish (US)
Article number41
JournalProteome Science
Volume8
DOIs
StatePublished - Jul 27 2010
Externally publishedYes

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Liquid chromatography
Tandem Mass Spectrometry
Liquid Chromatography
Proteomics
Mass spectrometry
Rats
Polyacrylamide Gel Electrophoresis
Brain
Proteins
GABA Plasma Membrane Transport Proteins
HSP70 Heat-Shock Proteins
Glial Fibrillary Acidic Protein
Immunoblotting
Septins
Chemical activation
Synaptotagmins
HSP90 Heat-Shock Proteins
Occipital Lobe
Parietal Lobe
Mitochondria

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Proteomic analysis of proteins expressing in regions of rat brain by a combination of SDS-PAGE with nano-liquid chromatography-quadrupole-time of flight tandem mass spectrometry. / Katagiri, Tomoki; Hatano, Naoya; Aihara, Masamune; Kawano, Hiroo; Okamoto, Mariko; Liu, Ying; Izumi, Tomonori; Maekawa, Tsuyoshi; Nakamura, Shoji; Ishihara, Tokuhiro; Shirai, Mutsunori; Mizukami, Yoichi.

In: Proteome Science, Vol. 8, 41, 27.07.2010.

Research output: Contribution to journalArticle

Katagiri, Tomoki ; Hatano, Naoya ; Aihara, Masamune ; Kawano, Hiroo ; Okamoto, Mariko ; Liu, Ying ; Izumi, Tomonori ; Maekawa, Tsuyoshi ; Nakamura, Shoji ; Ishihara, Tokuhiro ; Shirai, Mutsunori ; Mizukami, Yoichi. / Proteomic analysis of proteins expressing in regions of rat brain by a combination of SDS-PAGE with nano-liquid chromatography-quadrupole-time of flight tandem mass spectrometry. In: Proteome Science. 2010 ; Vol. 8.
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abstract = "Background: Most biological functions controlled by the brain and their related disorders are closely associated with activation in specific regions of the brain. Neuroproteomics has been applied to the analysis of whole brain, and the general pattern of protein expression in all regions has been elucidated. However, the comprehensive proteome of each brain region remains unclear.Results: In this study, we carried out comparative proteomics of six regions of the adult rat brain: thalamus, hippocampus, frontal cortex, parietal cortex, occipital cortex, and amygdala using semi-quantitative analysis by Mascot Score of the identified proteins. In order to identify efficiently the proteins that are present in the brain, the proteins were separated by a combination of SDS-PAGE on a C18 column-equipped nano-liquid chromatograph, and analyzed by quadrupole-time of flight-tandem-mass spectrometry. The proteomic data show 2,909 peptides in the rat brain, with more than 200 identified as region-abundant proteins by semi-quantitative analysis. The regions containing the identified proteins are membrane (20.0{\%}), cytoplasm (19.5{\%}), mitochondrion (17.1{\%}), cytoskeleton (8.2{\%}), nucleus (4.7{\%}), extracellular region (3.3{\%}), and other (18.0{\%}). Of the identified proteins, the expressions of glial fibrillary acidic protein, GABA transporter 3, Septin 5, heat shock protein 90, synaptotagmin, heat shock protein 70, and pyruvate kinase were confirmed by immunoblotting. We examined the distributions in rat brain of GABA transporter 3, glial fibrillary acidic protein, and heat shock protein 70 by immunohistochemistry, and found that the proteins are localized around the regions observed by proteomic analysis and immunoblotting. IPA analysis indicates that pathways closely related to the biological functions of each region may be activated in rat brain.Conclusions: These observations indicate that proteomics in each region of adult rat brain may provide a novel way to elucidate biological actions associated with the activation of regions of the brain.",
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AU - Katagiri, Tomoki

AU - Hatano, Naoya

AU - Aihara, Masamune

AU - Kawano, Hiroo

AU - Okamoto, Mariko

AU - Liu, Ying

AU - Izumi, Tomonori

AU - Maekawa, Tsuyoshi

AU - Nakamura, Shoji

AU - Ishihara, Tokuhiro

AU - Shirai, Mutsunori

AU - Mizukami, Yoichi

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