Absolute quantification of human proteome by information based quantitative proteomics

• Project/Area Number: 22710186
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Genome biology
• Research Institution: Kyushu University
• Principal Investigator: MATSUMOTO Masaki 九州大学, 生体防御医学研究所 (60380531)
• Project Period (FY): 2010 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2011: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2010: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: プロテオーム / プロテオミクス / 絶対定量 / ネットワーク解析 / システム生物学

Research Abstract

Due to the huge dynamic range of proteins amount, the detection of proteins expressed in low copy number by conventional proteomics based on mass-spectrometry is a major challenge. To solve this issue, we developed novel method to detect and quantitate human proteins by the combination of MRM, target proteomics and recombinant proteins generated from cDNA library. Using this system, we obtained information about the absolute expression level of many proteins including low abundant proteins that were difficult to detect.

Research Products

• [Journal Article] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin (2012)
  • Author(s): Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
  • Journal Title: J. Proteome Res Volume: 11 Issue: 2 Pages: 796-807
  • DOI: 10.1021/pr200668y
  • Peer Reviewed
• [Journal Article] Genetic reevaluation of the role of F-box proteins in cyclin D1 degradation (2012)
  • Author(s): Kanie T, et al
  • Journal Title: Molecular and Cellular Biology Volume: 32 Issue: 3 Pages: 590-605
  • DOI: 10.1128/mcb.06570-11
  • Peer Reviewed
• [Journal Article] Chk1 phosphorylates the tumor suppressor Mig-6, regulating the activation of EGF signaling (2012)
  • Author(s): Liu N., Matsumoto M., Kitagawa K., Kotake Y., Suzuki S., Shirasawa S., Nakayama KI, Nakanishi M., Niida H., Kitagawa M.
  • Journal Title: EMBO Journal Volume: (In press)
  • Peer Reviewed
• [Journal Article] Protrudin serves as an adaptor molecule that connects KIF5 and its cargoes in vesicular transport during process formation (2011)
  • Author(s): Matsuzaki, F., Shirane, M., Matsumoto, M., & Nakayama, K.I
  • Journal Title: Mol. Biol. Cell Volume: 22 Issue: 23 Pages: 4602-4620
  • DOI: 10.1091/mbc.e11-01-0068
  • Peer Reviewed
• [Journal Article] Functional analyses of the activation loop of phototropin2 in Arabidopsis (2011)
  • Author(s): Inoue S, Matsushita T, Tomokiyo Y, Matsumoto M, Nakayama KI, Kinoshita T, Shimazaki K.
  • Journal Title: Plant Physiology Volume: 156 Issue: 1 Pages: 117-128
  • DOI: 10.1104/pp.111.175943
  • Peer Reviewed
• [Journal Article] TRIM8 regulates Nanog via Hsp90 beta-mediated nuclear translocation of STAT3 in embryonic stem cells (2011)
  • Author(s): Okumura, F., Okumura, A.J., Matsumoto, M., Nakayama, K.I. and Hatakeyama, S.
  • Journal Title: BBA-Mol. Cell Res. Volume: 1813 Issue: 10 Pages: 1784-1792
  • DOI: 10.1016/j.bbamcr.2011.05.013
  • Peer Reviewed
• [Journal Article] Proteome of ubiquitin/MVB pathway : possible involvement of iron-induced ubiquitylation of transferrin receptor in lysosomal degradation (2011)
  • Author(s): Tachiyama R, Ishikawa D, Matsumoto M, Nakayama KI, Yoshimori T, Yokota S, Himeno M, Tanaka Y, Fujita H
  • Journal Title: Genes Cells Volume: 16 Issue: 4 Pages: 448-66
  • DOI: 10.1111/j.1365-2443.2011.01499.x
  • Peer Reviewed
• [Journal Article] Proteome of ubiquitin/MVB pathway : possible involvement of iron-induced ubiquitylation of transferrin receptor in lysosomal degradation. (2011)
  • Author(s): Tachiyama R, Ishikawa D, Matsumoto M, Nakayama KI, Yoshimori T, Yokota S, Himeno M, Tanaka Y, Fujita H.
  • Journal Title: Genes Cells Volume: 16 Pages: 448-466
  • Peer Reviewed
• [Journal Article] Human proteins that specifically bind to 8-oxoguanine-containing RNA and their responses to oxidative stress (2010)
  • Author(s): Hayakawa H, Fujikane A, Ito R, Matsumoto M, Nakayama KI, Sekiguchi M.
  • Journal Title: Biochem Biophys Res. Commun Volume: 403 Issue: 2 Pages: 220-224
  • DOI: 10.1016/j.bbrc.2010.11.011
  • Peer Reviewed
• [Journal Article] Comparative analysis of human SRC-family kinase substrate specificity in vitro (2010)
  • Author(s): Takeda H, Kawamura Y, Miura A, Mori M, Wakamatsu A, Yamamoto J., Isogai T., Matsumoto M, Nakayama KI., Natsume T., Nomura N., Goshima N.
  • Journal Title: J. Proteome Res Volume: 9 Issue: 11 Pages: 5982-5993
  • DOI: 10.1021/pr100773t
  • Peer Reviewed
• [Journal Article] Phosphorylation of the chromodomain changes the binding specificity of Cbx2 for methylated histone H3 (2010)
  • Author(s): Hatano A, Matsumoto M, Higashinakagawa T, Nakayama KI.
  • Journal Title: Biochem Biophys Res. Commun Volume: 397 Issue: 1 Pages: 93-99
  • DOI: 10.1016/j.bbrc.2010.05.074
  • Peer Reviewed
• [Journal Article] Human proteins that specifically bind to 8-oxoguanine-containing RNA and their responses to oxidative stress. (2010)
  • Author(s): Hayakawa H, Fujikane A, Ito R, Matsumoto M, Nakayama KI, Sekiguchi M
  • Journal Title: Biochem Biophys Res Commun Volume: 403 Pages: 220-224
  • Peer Reviewed
• [Journal Article] Comparative analysis of human SRC-family kinase substrate specificity in vitro (2010)
  • Author(s): Takeda H., Kawamura Y., Miura A., Mori M., Wakamatsu A., Yamamoto J., Isogai T., Matsumoto M., Nakayama KI., Natsume T., Nomura N., Goshim N.
  • Journal Title: J Proteome Res Volume: 9 Pages: 5982-93
  • Peer Reviewed
• [Journal Article] Phosphorylation of the chromodomain changes the binding specificity of Cbx2 for methylated histone H3. (2010)
  • Author(s): Hatano A, Matsumoto M, Higashinakagawa T, Nakayama KI
  • Journal Title: Biochem Biophys Res Commun. Volume: 397 Pages: 93-99
  • Peer Reviewed
• [Presentation] MS定量解析および大規模データ解析 (2011)
  • Author(s): 松本雅記
  • Organizer: 日本生化学会
  • Place of Presentation: 京都・国立国際会館
  • Year and Date: 2011-09-13
• [Presentation] MS定量解析および大規模データ解析 (2011)
  • Author(s): 松本雅記
  • Organizer: 日本生化学会
  • Place of Presentation: 京都・国立国際会館(招待講演)
  • Year and Date: 2011-09-13
• [Presentation] 定量プロテオミクスによる生命科学研究の新展開 (2011)
  • Author(s): 松本雅記、中山敬一
  • Organizer: 日本ヒトプロテオーム学会
  • Place of Presentation: 新潟・朱鷺メッセ
  • Year and Date: 2011-07-19
• [Presentation] 定量プロテオミクスによる生命科学研究の新展開 (2011)
  • Author(s): 松本雅記、中山敬一
  • Organizer: 日本ヒトプロテオーム学会
  • Place of Presentation: 新潟・朱鷺メッセ(招待講演)
  • Year and Date: 2011-07-19
• [Presentation] 定量プロテオミクスが拓く生命科学研究の新展開 (2010)
  • Author(s): 松本雅記
  • Organizer: 第33回日本分子生物学会年会・第83回日本生化学会大会合同大会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 2010-12-08
• [Presentation] 情報基盤ターゲット・プロテオミクスを用いたヒト・プロテオームの絶対定量 (2010)
  • Author(s): 松本雅記、五島直樹、夏目徹、中山敬一
  • Organizer: 日本プロテオーム学会
  • Place of Presentation: 東京ベイホテル東急
  • Year and Date: 2010-07-27
• [Remarks]
  • URL: http://www.bioreg.kyushu-u.ac.jp/saibou/index.html
• [Remarks]
  • URL: http://www.bioreg.kyushu-u.ac.jp/saibou/index.html