Development of a platform for proteome analysis of clinical FFPE samples

• Project/Area Number: 26505005
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: オミクス計測科学
• Research Institution: Kyoto University
• Principal Investigator: Wakabayashi Masaki 京都大学, 薬学研究科, 助教 (70552024)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2015: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: プロテオミクス / FFPE / LC-MS / プロテオーム / HE染色 / 高感度LC/MS / リン酸化プロテオミクス / 高感度分析

Outline of Final Research Achievements

This study provided a novel protein-extraction method and highly sensitive LC-MS system suitable for proteome profiling of minuscule FFPE tissue slices. This system can be utilized as a standard platform for FFPE proteome analysis. It was suggested that hematoxylin and eosin staining caused loss of proteins from FFPE tissues. Therefore, more detailed analysis is required for evaluating whether HE-stained FFPE tissue slices are suitable for proteome profiling.

Research Products

• [Journal Article] A conditional proteomics approach to identify proteins involved in zinc homeostasis (2016)
  • Author(s): T. Miki, M. Awa, Y. Nishikawa, S. Kiyonaka, M. Wakabayashi, Y. Ishihama, I. Hamachi
  • Journal Title: Nature Methods Volume: 13 Issue: 11 Pages: 931-937
  • DOI: 10.1038/nmeth.3998
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Extended coverage of singly and multiply phosphorylated peptides from a single titanium dioxide microcolumn (2015)
  • Author(s): Masaki Wakabayashi, Yutaka Kyono, Naoyuki Sugiyama, Yasushi Ishihama
  • Journal Title: Analytical chemistry Volume: 87 Issue: 20 Pages: 10213-21
  • DOI: 10.1021/acs.analchem.5b01216
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Hydrophilic Interaction Chromatography Using Meter-scale Monolithic Silica Capillary Column for Proteomics LC-MS. (2014)
  • Author(s): Horie K, Kamakura T, Ikegami T, Wakabayashi M, Kato T, Tanaka N, Ishihama Y.
  • Journal Title: Anal Chem Volume: 86 Issue: 8 Pages: 3817-24
  • DOI: 10.1021/ac4038625
  • Peer Reviewed
• [Journal Article] Large-Scale Identification of Phosphorylation Sites for Profiling Protein Kinase Selectivity. (2014)
  • Author(s): Imamura H, Sugiyama N, Wakabayashi M, Ishihama Y.
  • Journal Title: J Proteome Res. Volume: 13 Issue: 7 Pages: 3410-19
  • DOI: 10.1021/pr500319y
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Single cell proteome profiling using highly sensitive LC-MS system and In-capillary sample preparation method (2016)
  • Author(s): Masaki Wakabayashi, Yasushi Ishihama
  • Organizer: AOHUPO 2016
  • Place of Presentation: Nantou (Taiwan)
  • Year and Date: 2016-09-22
  • Int'l Joint Research
• [Presentation] Single-cell proteome profiling: Innovations in sample preparation (2016)
  • Author(s): Masaki Wakabayashi, Yasushi Ishihama
  • Organizer: 15th Human Proteome Organization World Congress
  • Place of Presentation: Taipei (Taiwan)
  • Year and Date: 2016-09-18
  • Int'l Joint Research
• [Presentation] 1細胞解析を指向した超高感度プロテオーム解析 プラットフォームの開発 (2016)
  • Author(s): 若林 真樹、杉山 直幸、石濱 泰
  • Organizer: 第29回バイオメディカル分析科学シンポジウム
  • Place of Presentation: 京都大学桂キャンパス（京都）
  • Year and Date: 2016-09-02
• [Presentation] 極微量試料のプロテオーム解析手法の開発 ～1細胞プロテオーム解析プラットフォームの構築を目指して～ (2016)
  • Author(s): 若林 真樹
  • Organizer: 日本プロテオーム学会2016年大会
  • Place of Presentation: 北里大学薬学部（東京）
  • Year and Date: 2016-07-28
• [Presentation] 極微量プロテオーム解析手法の開発～1細胞プロテオーム解析への挑戦～ (2016)
  • Author(s): 若林真樹
  • Organizer: 北里疾患プロテオーム研究会
  • Place of Presentation: 北里大学理学部（神奈川）
  • Year and Date: 2016-03-25
  • Invited
• [Presentation] 単一細胞プロテオーム解析技術の開発 (2015)
  • Author(s): 若林真樹
  • Organizer: BMAS2015
  • Place of Presentation: 長崎大学（長崎）
  • Year and Date: 2015-08-21
• [Presentation] Single-cell proteome profiling: Innovations in sample preparation (2015)
  • Author(s): Masaki Wakabayashi, Jordan T Aerts, Stanislav S Rubakhin, Yasushi Ishihama, Jonathan V Sweedler
  • Organizer: 日本プロテオーム学会2015年会
  • Place of Presentation: くまもと森都心プラザ（熊本）
  • Year and Date: 2015-07-23
• [Presentation] Single cell proteome profiling using highly sensitive LC-MS system and In-capillary sample preparation (2015)
  • Author(s): Masaki Wakabayashi, Jordan T Aerts, Elena V romanova, Stanislav S Rubakhin, Yasushi Ishihama, Jonathan V Sweedler
  • Organizer: 63rd American society for mass spectrometry conference
  • Place of Presentation: St. Louis, United States
  • Year and Date: 2015-05-31
• [Presentation] 超高感度LC-MSシステムを用いた単一細胞プロテオーム解析 (2015)
  • Author(s): 若林真樹、Jordan T Aerts、Stanislav S Rubakhin、石濱泰、Jonathan V Sweedler
  • Organizer: 日本薬学会第135年会
  • Place of Presentation: 神戸学院大学
  • Year and Date: 2015-03-25 – 2015-03-28
  • Invited
• [Presentation] Downscaling proteome profiling: toward single cell proteomics (2014)
  • Author(s): Masaki Wakabayashi, Jordan T Aerts, Stanislav S Rubakhin, Yasushi Ishihama, Jonathan V Sweedler
  • Organizer: 14th Asia-Pacific International Symposium on Microscale Separations and Analysis
  • Place of Presentation: 京大桂キャンパス
  • Year and Date: 2014-12-07 – 2014-12-10
• [Presentation] 1細胞プロテオーム解析への挑戦 (2014)
  • Author(s): 若林真樹、Jordan T Aerts、Stanislav S Rubakhin、石濱泰、Jonathan V Sweedler
  • Organizer: 第87回日本生化学会大会
  • Place of Presentation: 京都国際会館
  • Year and Date: 2014-10-15 – 2014-10-18
  • Invited
• [Presentation] 単一細胞プロテオーム解析への挑戦 (2014)
  • Author(s): 若林真樹、Jordan T Aerts、 Stanislav S Rubakhin、石濱泰、Jonathan V Sweedler
  • Organizer: BMAS2014 第27回バイオメディカル分析科学シンポジウム
  • Place of Presentation: 帝京大学 板橋キャンパス
  • Year and Date: 2014-08-20 – 2014-08-21