Basic Information

Faculty

• Faculty of Pharmaceutical Sciences

Professional Memberships

• ヒトプロテオーム機構
• American Society for Mass Spectrometry
• 日本分子生物学会
• 日本質量分析学会
• クロマトグラフィー科学会
• 日本薬学会
• 日本プロテオーム学会

Academic Degree

• 23 Mar. 2022

  京都大学博士（薬科学）
• 23 Mar. 2022

  京都大学博士（薬学）
• 修士（薬科学）(京都大学)

Research History

• From Jul. 2024, To Dec. 2024

  Swiss Federal Institute of Technology in Zurich, Academic Guest
• From May 2019, To Mar. 2022

  Graduate School of Pharmaceutical Sciences, Kyoto University, Molecular Cellular Bioanalysis, Assistant Professor
• From Apr. 2022, To Present

  京都大学大学院薬学研究科, 創発医薬科学専攻生体分子計測学分野, 助教

ID,URL

• ORCID ID

  0000-0002-0634-3990

• J-Global ID

  201901014265841461

researchmap URL

• https://researchmap.jp/ogata_kk

Research

Research Topics, Overview of the research

• Research Topics

  Development of analytical strategy for phosphoproteomics and its application to the analysis of protein functions

• Overview of the research

  My research field is phosphoproteome analysis and I'm conducting the development of novel analytical strategy. My main research target is to elucidate the relationships between phosphoproteome and protein structures and between phosphoproteome and protein functions.

Research Interests

• Protein phosphorylation
• Liquid chromatography
• Mass spectrometry
• Proteomics

Research Areas

• Life sciences, Genomics

Papers

• Bottom-up proteomics under acidic conditions using protease type XIII from Aspergillus saitoi

  Ryota Tomioka; Ayana Tomioka; Kosuke Ogata; Yasushi Ishihama

  01 Jun. 2025

  
• Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler

  Asato Maeda; Kosuke Ogata; Yasushi Ishihama

  12 May 2025

  
• Visible light-mediated photocatalytic coupling between tetrazoles and carboxylic acids for biomolecule labelling

  Takuro Matsuoka; Ryosuke Takasaki; Hiroki Akiba; Kosuke Ogata; Akira Hattori; Norihito Arichi; Hideaki Kakeya; Sho Yamasaki; Yasushi Ishihama; Hiroaki Ohno; Shinsuke Inuki

  Chemical Communications, 2025

  
• Receptor-independent regulation of Gα13 by alpha-1-antitrypsin C-terminal peptides

  Yonghak Park; Shigeyuki Matsumoto; Kosuke Ogata; Biao Ma; Ryo Kanada; Yuta Isaka; Norihito Arichi; Xiaowen Liang; Ritsuko Maki; Tohru Kozasa; Yasushi Okuno; Hiroaki Ohno; Yasushi Ishihama; Fumiko Toyoshima

  Journal of Biological Chemistry, Feb. 2025

  
• High-Recovery Desalting Tip Columns for a Wide Variety of Peptides in Mass Spectrometry-Based Proteomics

  Eisuke Kanao; Shunsuke Tanaka; Ayana Tomioka; Kosuke Ogata; Tetsuya Tanigawa; Takuya Kubo; Yasushi Ishihama

  Analytical Chemistry, 31 Dec. 2024

  Access this paper :

  
• AP-1B regulates interactions of epithelial cells and intraepithelial lymphocytes in the intestine

  Ryohtaroh Matsumoto; Kosuke Ogata; Daisuke Takahashi; Yusuke Kinashi; Takahiro Yamada; Ryo Morita; Keisuke Tanaka; Kouya Hattori; Mayumi Endo; Yumiko Fujimura; Nobuo Sasaki; Hiroshi Ohno; Yasushi Ishihama; Shunsuke Kimura; Koji Hase

  Cellular and Molecular Life Sciences, Dec. 2024

  
• UniScore, a unified and universal measure for peptide identification by multiple search engines

  Tsuyoshi Tabata; Akiyasu C Yoshizawa; Kosuke Ogata; Chih-Hsiang Chang; Norie Araki; Naoyuki Sugiyama; Yasushi Ishihama

  Molecular & Cellular Proteomics, 13 Oct. 2024

  
• Leveraging pretrained deep protein language model to predict peptide collision cross section

  Ayano Nakai-Kasai; Kosuke Ogata; Yasushi Ishihama; Toshiyuki Tanaka

  Communications Chemistry, 06 May 2025

  
• Prediction of Protein Half-lives from Amino Acid Sequences by Protein Language Models

  Tatsuya Sagawa; Eisuke Kanao; Kosuke Ogata; Koshi Imami; Yasushi Ishihama

  14 Sep. 2024

  
• Highly sequence-specific, timing-controllable m6A demethylation by modulating RNA-binding affinity of m6A erasers

  Kenko Otonari; Yuri Asami; Kosuke Ogata; Yasushi Ishihama; Shiroh Futaki; Miki Imanishi

  Chemical Communications, 2025

  
• Protein N-Terminomics Reveals Major Proteases in Regulating Beige Adipocyte Differentiation

  Hsin-Yi Chang; Chih-Hsiang Chang; Hiroshi Nishida; Kaho Takamuro; Kosuke Ogata; Kuan-Chieh Peng; Li-Chun Lin; Yii-Jwu Lo; Tsui-Chin Huang; Yasushi Ishihama

  02 Aug. 2022

  
• Quantitation of Host Cell Proteins by Capillary LC/IMS/MS/MS in Combination with Rapid Digestion on Immobilized Trypsin Column Under Native Conditions

  Ryota Tomioka; Kosuke Ogata; Yasushi Ishihama

  Mass Spectrometry, 2024, Peer-reviewed

  Access this paper :

  
• In vitro reconstitution of epigenetic reprogramming in the human germ line

  Yusuke Murase; Ryuta Yokogawa; Yukihiro Yabuta; Masahiro Nagano; Yoshitaka Katou; Manami Mizuyama; Ayaka Kitamura; Pimpitcha Puangsricharoen; Chika Yamashiro; Bo Hu; Ken Mizuta; Taro Tsujimura; Takuya Yamamoto; Kosuke Ogata; Yasushi Ishihama; Mitinori Saitou

  Nature, 20 May 2024, Peer-reviewed

  
• Retention time prediction for post-translationally modified peptides: Ser, Thr, Tyr-phosphorylation

  Taylor Battellino; Darien Yeung; Haley Neustaeter; Vic Spicer; Kosuke Ogata; Yasushi Ishihama; Oleg V. Krokhin

  Journal of Chromatography A, Mar. 2024, Peer-reviewed

  
• Extending the Coverage of Lys-C/Trypsin-Based Bottom-up Proteomics by Cysteine S-Aminoethylation

  Ryota Tomioka; Ayana Tomioka; Kosuke Ogata; Hsin-Ju Chan; Li-Yu Chen; Ulises H. Guzman; Yue Xuan; Jesper V. Olsen; Yu-Ju Chen; Yasushi Ishihama

  Journal of the American Society for Mass Spectrometry, 29 Jan. 2024, Peer-reviewed

  
• One thousand samples per day capillary-flow LC/MS/MS for high-speed, high-sensitivity and in-depth proteomics

  Ayana Tomioka; Ryota Tomioka; Issei Mori; Yosuke Isobe; Makoto Arita; Koshi Imami; Eisuke Kanao; Kosuke Ogata; Yasushi Ishihama

  07 Jun. 2023

  
• Motif-Targeting Phosphoproteome Analysis of Cancer Cells for Profiling Kinase Inhibitors

  Kosuke Ogata; Shunsuke Takagi; Naoyuki Sugiyama; Yasushi Ishihama

  Cancers, 23 Dec. 2022, Peer-reviewed, Lead author

  
• Acetic Acid Ion Pairing Additive for Reversed-Phase HPLC Improves Detection Sensitivity in Bottom-up Proteomics Compared to Formic Acid

  Taylor Battellino; Kosuke Ogata; Victor Spicer; Yasushi Ishihama; Oleg Krokhin

  Journal of Proteome Research, 08 Dec. 2022, Peer-reviewed

  
• Temperature Dependence of Retention Behavior of Phosphorylated Peptides in Ion-Pair Reversed-Phase Liquid Chromatography

  Kosuke OGATA; Yasushi ISHIHAMA

  CHROMATOGRAPHY, 20 Oct. 2022, Peer-reviewed, Lead author

  
• Motif-Centric Phosphoproteomics to Target Kinase-Mediated Signaling Pathways

  Chia-Feng Tsai; Kosuke Ogata; Naoyuki Sugiyama; Yasushi Ishihama

  Cell Reports Methods, 24 Jan. 2022, Peer-reviewed, Lead author

  Access this paper :

  
• CoolTip: Low-Temperature Solid-Phase Extraction Microcolumn for Capturing Hydrophilic Peptides and Phosphopeptides

  Kosuke Ogata; Yasushi Ishihama

  Molecular & Cellular Proteomics, Nov. 2021, Peer-reviewed, Lead author

  Access this paper :

  
• IRAK1-Dependent Regnase-1-14-3-3 Complex Formation Controls Regnase-1-Mediated mRNA Decay

  Kotaro Akaki; Kosuke Ogata; Yuhei Yamauchi; Noriki Iwai; Ka Man Tse; Fabian Hia; Atsushi Mochizuki; Yasushi Ishihama; Takashi Mino; Osamu Takeuchi

  eLife, 12 Oct. 2021, Peer-reviewed

  Access this paper :

  
• Phosphatidylserine-Deficient Small Extracellular Vesicle is a Major Somatic Cell-Derived sEV Subpopulation in Blood

  Akihiro Matsumoto; Yuki Takahashi; Kosuke Ogata; Shimpei Kitamura; Naoki Nakagawa; Aki Yamamoto; Yasushi Ishihama; Yoshinobu Takakura

  iScience, 20 Aug. 2021, Peer-reviewed

  
• Nanoscale Solid-Phase Isobaric Labeling for Multiplexed Quantitative Phosphoproteomics

  Kosuke Ogata; Chia-Feng Tsai; Yasushi Ishihama

  Journal of Proteome Research, 06 Aug. 2021, Peer-reviewed, Lead author

  Access this paper :

  
• Sequence-Specific Model for Predicting Peptide Collision Cross Section Values in Proteomic Ion Mobility Spectrometry

  Chih-Hsiang Chang; Darien Yeung; Victor Spicer; Kosuke Ogata; Oleg Krokhin; Yasushi Ishihama

  Journal of Proteome Research, 02 Jul. 2021, Peer-reviewed

  
• Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry

  Kosuke Ogata; Chih-Hsiang Chang; Yasushi Ishihama

  Mass Spectrometry, 2020, Peer-reviewed, Lead author

  Access this paper :

  
• Extending the Separation Space with Trapped Ion Mobility Spectrometry Improves the Accuracy of Isobaric Tag-Based Quantitation in Proteomic LC/MS/MS.

  Kosuke Ogata; Yasushi Ishihama

  Analytical Chemistry, 16 Jun. 2020, Peer-reviewed, Lead author

  Access this paper :

  
• Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS

  Kosuke OGATA; Oleg V. KROKHIN; Yasushi ISHIHAMA

  Analytical Sciences, 10 Sep. 2018, Peer-reviewed, Lead author

  Access this paper :

  
• Ubiquitination at the lysine 27 residue of the parkin ubiquitin-like domain is suggestive of a new mechanism of parkin activation

  Jun-Yi Liu; Tsuyoshi Inoshita; Kahori Shiba-Fukushima; Shigeharu Yoshida; Kosuke Ogata; Yasushi Ishihama; Yuzuru Imai; Nobutaka Hattori

  Human Molecular Genetics, 21 Mar. 2022, Peer-reviewed

  

Misc.

• Development of high-speed and high-sensitivity capillary LC/MS/MS system for ultra-high throughput proteomics

  小形公亮; 富岡郁那; 富岡亮太; 垣内大斗; 森一成; 森一成; 有田誠; 有田誠; 今見考志; 金尾英佑; 金尾英佑; 石濱泰; 石濱泰

  日本薬学会年会要旨集(Web), 2024

  
• Spatial Proteome Imaging by Machine-gun Proteomics

  富岡郁那; 富岡亮太; 小形公亮; 森一晟; 森一晟; 有田誠; 有田誠; 今見孝志; 杉山直幸; 石濱泰; 石濱泰

  質量分析総合討論会講演要旨集, 2023

  
• Deep profiling of proteome structural changes with enzymatic reactions

  Kosuke Ogata; Asato Maeda; Yuka Muramarsu; Naoyuki Sugiyama; Yasushi Ishihama

  HUPO2022, Dec. 2022

  
• カルシウムイオンの添加によるリン酸化タンパク質のトリプシン消化効率の改善

  小形公亮; 石濱泰

  第45回日本分子生物学会年会, Dec. 2022

  
• 小さなセルの大きな世界-高感度分析技術が照らしだすシングルセルプロテオーム

  小形公亮; 石濱泰

  化学, 2022

  
• Sensing protein conformational changes by in vitro phosphorylation tagging

  前田朝登; 小形公亮; 杉山直幸; 石濱泰

  日本薬学会年会要旨集(Web), 2022

  
• Adding New Dimension to Peptide Separation with Ion Mobility Spectrometry

  小形公亮; CHANG Chih-Hsiang; YEUNG Darien; SPICER Victor; KROKHIN Oleg; 石濱泰; 石濱泰

  質量分析総合討論会講演要旨集, 2022

  
• Development of High-Sensitivity/High-Throughput Proteomics Systems for Minute Sample Analysis

  中井郁那; 富岡亮太; 杉山直幸; 小形公亮; 石濱泰

  質量分析総合討論会講演要旨集, 2022

  
• Development of protease enrichment methods using cleaved substrate peptide probes

  渡邉佑太; 新苗智也; 小形公亮; 杉山直幸; 石濱泰

  日本薬学会年会要旨集(Web), 2021

  
• Peptide ion mobility prediction based on the sequence-specific amino acid contributions

  小形公亮; CHANG Chih-Hsiang; YEUNG Darien; SPICER Victor; KROKHIN Oleg; 石濱泰; 石濱泰

  バイオメディカル分析科学シンポジウム講演要旨集, 2021

  
• Development of a novel proteome analysis method utilizing nanoLC/ion mobility spectrometry/MS

  中井郁那; 富岡亮太; 杉山直幸; 小形公亮; 石濱泰

  バイオメディカル分析科学シンポジウム講演要旨集, 2021

  
• Decomposition of MS/MS spectrograms from DIA proteomics for protein identification and quantitation

  町田和典; 上村京也; 田畑剛; 小形公亮; 吉沢明康; 吉井和佳; 田中利幸; 石濱泰

  日本薬学会年会要旨集(Web), 2022

  
• Effect of Phosphorylation on the Collision Cross Sections of Peptide Ions in Ion Mobility Spectrometry

  Ogata Kosuke; Chang Chih-Hsiang; Ishihama Yasushi

  Mass Spectrometry (Web), 2021

  Access this misc :

  
• Trypsin Limited Proteolysis Strategy towards in-depth Structural Proteomics

  Kosuke Ogata; Yasushi Ishihama

  68th ASMS Conference on Mass Spectrometry and Allied Topics, Jun. 2020

  
• Shotgun Proteomics with Temperature Controlled Reversed Phase Liquid Chromatography

  K.Ogata; R.Tomioka; Y.Ishihama

  第68回 質量分析総合討論会, May 2020

  
• Development of Proteome Analysis Exclusively Using Precursor Ion Information

  中井郁那; 富岡亮太; 杉山直幸; 小形公亮; 石濱泰

  質量分析総合討論会講演要旨集, 2020

  
• Peptide identification by LC/MS-based Proteomics without product ion information

  中井郁那; 富岡亮太; 杉山直幸; 小形公亮; 石濱泰

  日本薬学会年会要旨集(CD-ROM), 2020

  
• Gradient Refocusing Strategies for Shotgun Proteomics with Meter-Scale Monolithic Silica Capillary Columns

  Kosuke Ogata; Ryota Tomioka; Michio Funahashi; Naoyuki Sugiyama; Yasushi Ishihama

  8th Asia-Oceania Mass Spectrometry Conference, Jan. 2020

  
• メートル長モノリス型シリカカラムとグラジエント再濃縮を用いた高深度プロテオミクス

  小形公亮; 富岡亮太; 舟橋充央; 杉山直幸; 石濱泰

  第30回クロマトグラフィー科学会議, Dec. 2019

  
• In-depth Proteome Analysis Using Meter-Scale Monolithic Silica Capillary Columns with Subsequent Gradient Refocusing

  Kosuke Ogata; Ryota Tomioka; Michio Funahashi; Naoyuki Sugiyama; Yasushi Ishihama

  49th International Symposium on High Performance Liquid Phase Separations and Related Techniques, Dec. 2019

  
• プロテオミクスLC/MSにおけるリン酸化ペプチドの保持挙動

  Kosuke Ogata; Naoyuki Sugiyama; Oleg V. Krokhin; Yasushi Ishihama

  第17回次世代を担う若手のためのフィジカル・ファーマフォーラム, Sep. 2019

  
• イオンモビリティ分離により加速する高深度ヒトプロテオーム解析

  Kosuke Ogata

  日本プロテオーム学会2019年大会・第70回日本電気泳動学会総会合同大会, Jul. 2019, Invited

  
• プロテオミクスLC/MS/MSにおける高速化の検討

  富岡亮太; 舟橋充央; 小形公亮; 張心儀; 杉山直幸; 石濱泰

  日本薬学会第139年会, Mar. 2019

  
• Additional Separation Space by Trapped Ion Mobility Spectrometry Improves Accuracy of Isobaric Tag-based Quantitation

  Kosuke Ogata; Tomoya Niinae; Chia-Feng Tsai; Koshi Imami; Naoyuki Sugiyama; Yasushi Ishihama

  Keystone Symposium on Proteomics and its Application to Translational and Precision Medicine (D3), 2019

  
• Next generation StageTip for capturing extremely hydrophilic peptides

  Kosuke Ogata; Chia-Feng Tsai; Naoyuki Sugiyama; Yasushi Ishihama

  The 67th ASMS Conference on Mass Spectrometry and Allied Topics, 2019

  
• 逆相LC/MSにおけるリン酸化/非リン酸化ペプチドの溶出順序の逆転

  小形公亮; KROHKIN Oleg V.; 石濱泰

  バイオメディカル分析科学シンポジウム講演要旨集, 2018

  
• High Resolution Peptide Separation for Illuminating Human Proteome

  Yasushi Ishihama; Kosuke Ogata; Chih-Hsiang Chang; Koshi Imami; Naoyuki Sugiyama

  HUPO2018, 2018

  
• Protein chromatography for bottom-up proteomics to extend the proteome coverage

  Kosuke Ogata; Michio Funahashi; Hsin-Yi Chang; Naoyuki Sugiyama; Yasushi Ishihama

  The 66th ASMS Conference on Mass Spectrometry and Allied Topics, 2018

  
• キナーゼ阻害薬と定量的リン酸化プロテオミクスを用いたPKA基質探索

  新苗智也; 小形公亮; 今村春菜; 若林真樹; 杉山直幸; 石濱泰

  第65回質量分析総合討論会, 2017

  
• マルチプレックス解析:深度とスループットの両立

  小形公亮; TSAI Chia‐Feng; 若林真樹; 杉山直幸; 石濱泰

  日本プロテオーム学会大会プログラム・抄録集, 2017

  
• Highly sensitive quantitative phosphoproteomics and primary-sequence-based scoring reveals putative substrates of ERK.

  Kosuke Ogata; Haruna Imamura; Chia-Feng Tsai; Masaki Wakabayashi; Naoyuki Sugiyama; Yasushi Ishihama

  16th Human Proteome Organisation World Congress, 2017

  
• High sensitivity and high throughput phosphoproteomics with micro-scale TMT labeling.

  Kosuke Ogata; Chia-Feng Tsai; Masaki Wakabayashi; Naoyuki Sugiyama; Yasushi Ishihama

  21st International Mass Spectrometry Conference, 2016

  
• 定量的リン酸化プロテオミクスによるがん細胞株大規模プロファイリング

  高橋知里; 矢崎達也; 小形公亮; 佐藤義明; 木村剛之; 小田吉哉; 若林真樹; 杉山直幸; 石濱泰

  バイオメディカル分析科学シンポジウム講演要旨集, 21 Aug. 2015

  
• Phosphoproteomic profiling of molecular-targeted drugs by motif-targeting quantitation.

  Kosuke Ogata; Tatsuya Yazaki; Masaki Wakabayashi; Naoyuki Sugiyama; Yasushi Ishihama

  The 13th Annual Meeting of The Japanese Proteomics Society, 2015

  
• ターゲットプロテオミクスによるリン酸化シグナル動態解析

  矢崎達也; 高木俊輔; 小形公亮; 若林真樹; 杉山直幸; 石濱泰

  第25回クロマトグラフィー科学会議, 2014

  
• Motif-targeting phosphopeptide enrichment for quantitative phosphoproteome analysis

  Shunsuke Takagi; Tatsuya Yazaki; Kosuke Ogata; Masaki Wakabayashi; Naoyuki Sugiyama; Yasushi Ishihama

  13th Human Proteome Organization World Congress, 2014

  
• Profiling of molecular-targeted drugs by motif-targeted phosphoproteomics

  Kosuke Ogata; Tatsuya Yazaki; Yu Hayashi; Masaki Wakabayashi; Naoyuki Sugiyama; Yasushi Ishihama

  The 135th Annual Meeting of Pharmaceutical Society of Japan in Kobe, 2014

  
• Kinase Phosphorylation Motif-Targeting Phosphoproteomics for Elucidation of Signaling Pathways

  小形公亮; TSAI Chia-Feng; 杉山直幸; 石濱泰; 石濱泰

  日本分子生物学会年会プログラム・要旨集(Web), 01 Dec. 2021

  

Presentations

• 限定的酵素反応に基づくタンパク質局所構造変化の包括的解析

  小形 公亮; 平沼 侑奈; 村松 邑香; 前田 朝登; 石濱 泰

  第32回クロマトグラフィーシンポジウム, 16 May 2025

  
• Proteomic analysis of protein conformational changes based on the in vitro kinase reaction

  Kosuke Ogata; Asato Maeda; Naoyuki Sugiyama; Yasushi Ishihama

  EMBL Conference Quantitative biology to molecular mechanisms, 21 Nov. 2024

  
• プロテオミクスに基づく大規模ペプチドイオン移動度解析

  小形公亮

  第85回イオン反応研究会オンライン講演会, 25 Sep. 2024, Invited

  
• プロテオミクスLC/MSにおける電子励起解離の活用

  小形公亮; 谷口優斗; 柴田猛; 石濱泰

  JPrOS2024 & JSCP20th (22nd JHUPO & 20th JSCP), 28 Jun. 2024, Invited

  
• 逆相固相抽出・イオンモビリティ分離およびin vitroキナーゼ反応に基づく高感度定量リン酸化プロテオーム解析基盤の開発

  小形公亮

  JPrOS2024 & JSCP20th (22nd JHUPO & 20th JSCP), 26 Jun. 2024, Invited

  
• 電子誘起解離を用いたタンデム質量分析によるN末端プロテオミクス

  小形公亮; 谷口優斗; 柴田猛; 石濱泰

  第72回質量分析総合討論会, 10 Jun. 2024

  
• Re-exploring Zirconia Chromatography to Enhance Phosphoproteome Coverage

  Kosuke Ogata; Naoyuki Sugiyama; Yasushi Ishihama

  73rd Conference on Mass Spectrometry and Allied Topics, 06 Jun. 2024

  
• 瞬速プロテオミクスの創成：高速・高感度LC/MS/MSシステムの開発

  小形 公亮; 富岡 郁那; 富岡 亮太; 垣内 大斗; 森 一成; 有田 誠; 今見 考志; 金尾 英佑; 石濱 泰

  日本薬学会第144年会, 30 Mar. 2024, Invited

  
• 瞬速プロテオミクスの開発

  小形公亮; 富岡郁那; 富岡亮太; 石濱泰

  学変Aタンパク質寿命・第1回領域会議・ユビキチン研究会, 10 Feb. 2024

  
• 慢性B型肝炎ウイルス感染ヒト初代肝細胞においてIFNαがプロテオームに及ぼす影響

  Kosuke Ogata; Antonis Athanasiadis; Leon Seifer; George Dangas; Yingpu Yu; Christopher Jones; Taylor Shue; Alfred Jiang; Chenhui Zou; Corrine Quirk; Kelly-Marie Powel; William M. Schneider; Charles M. Rice; Ype P. de Jong; Yasushi Ishihama; Lefteris Michailidis

  第46回日本分子生物学会年会, 07 Dec. 2023

  
• 学習済み大規模タンパク質言語モデルによるペプチドのイオン移動度の予測

  小形公亮; 中井彩乃; 田中利幸; 石濱泰

  第43回キャピラリー電気泳動シンポジウム (SCE2023), 01 Dec. 2023

  
• 酵素反応効率に基づくプロテオーム規模基質タンパク質構造評価法の開発

  小形 公亮; 前田 朝登; 村松 邑香; 杉山 直幸; 石濱 泰

  第34回クロマトグラフィー科学会議, 27 Oct. 2023

  
• Ultrahigh throughput proteomics with high-speed and high-sensitivity LC/MS/MS system.

  Ayana Tomioka; Ryota Tomioka; Hiroto Kakiuchi; Issei Mori; Makoto Arita; Koshi Imami; Eisuke Kanao; Kosuke Ogata; Yasushi Ishihama

  3rd International BMS Symposium 2023 in Kyoto, 07 Oct. 2023, Invited

  
• 酵素反応による基質選択的サブプロテオーム解析法の開発

  小形公亮; 前田朝登; 村松邑香; 杉山直幸; 石濱泰

  第20回次世代を担う若手のためのフィジカル・ファーマフォーラム(PPF2023), 31 Aug. 2023

  
• Enzyme-based marking of proteome structures (EZMAP) to identify structural features of the proteome

  Kosuke Ogata; Asato Maeda; Yuka Muramatsu; Naoyuki Sugiyama; Yasushi Ishihama

  AOMSC-KSMS 2023, 20 Aug. 2023

  
• プロテオームにおける限定的タンパク質消化産物の選択的計測

  小形公亮; 村松邑香; 前田朝登; 杉山直幸; 石濱泰

  第35回バイオメディカル分析科学シンポジウム, 28 Jul. 2023

  
• 質量分析によるプロテオーム立体構造解析のための酵素反応の開拓

  小形公亮; 前田朝登; 村松邑香; 杉山直幸; 石濱泰

  日本プロテオーム学会 2023年大会, 26 Jul. 2023

  
• プロテオーム試料を基質とした酵素反応における基質タンパク質構造の影響

  小形公亮; 前田朝登; 村松邑香; 杉山直幸; 石濱泰

  第71回質量分析総合討論会, 17 May 2023

  
• Proteomic investigation of the effects of substrate protein structures on the enzymatic reactions

  Kosuke Ogata; Asato Maeda; Yuka Muramatsu; Naoyuki Sugiyama; Yasushi Ishihama

  11th AOHUPO and 7th AOAPO, 07 May 2023

  
• 酵素反応を用いた基質標的型構造プロテオミクス

  小形公亮

  第20回北里疾患プロテオーム研究会, 16 Mar. 2023, Invited

  
• イオンモビリティ分離が拓くプロテオミクスの新次元

  小形公亮

  第24回質量分析学会中部談話会, 02 Mar. 2023, Invited

  
• 酵素反応を用いた基質構造変化の包括的解析

  小形公亮; 前田朝登; 杉山直幸; 石濱泰

  第33回クロマトグラフィー科学会議, 03 Nov. 2022

  
• 高感度構造プロテオミクスのためのタンパク質フットプリント法の開発

  小形公亮; 前田朝登; 杉山直幸; 石濱泰

  第34回 バイオメディカル分析科学シンポジウム, 03 Sep. 2022

  
• タンパク質限定標識法による構造プロテオミクスの高感度化

  小形公亮; 前田朝登; 杉山直幸; 石濱泰

  日本プロテオーム学会2022年大会, 09 Aug. 2022

  
• イオンモビリティスペクトロメトリーによる新次元ペプチド分離

  小形公亮; Chih-Hsiang Chang; Darien Yeung; Victor Spicer; Oleg Krokhin; 石濱泰

  第70回質量分析総合討論会, 22 Jun. 2022

  
• Proteomic profiling of peptide collision cross-sections with trapped ion mobility spectrometry

  Kosuke Ogata; Chih-Hsiang Chang; Darien Yeung; Victor Spicer; Oleg Krokhin; Yasushi Ishihama

  The 10th Asia-Oceania Human Proteome Organization Congress, 30 Jun. 2021

  
• プロテオミクスLC/MSにおけるリン酸化ペプチドの保持挙動

  Kosuke Ogata

  PPF2019, 02 Sep. 2019

  
• Retention Order Reversal of Phosphorylated and Unphosphorylated Peptides in Reversed-Phase LC/MS

  Kosuke Ogata; Oleg V. Krokhin; 石濱 泰

  第 31回バイオメディカル分析科学シンポジウム, 28 Aug. 2018

  
• Multiplex Analysis: High Throughput and In-depth Quantitation

  Kosuke Ogata; Chia-Feng Tsai; Masaki Wakabayashi; Naoyuki Sugiyama; Yasushi Ishihama

  日本プロテオーム学会2017年大会, 26 Jul. 2017, Invited

  
• New labeling strategy with multiplex stable isotope tags for in-depth quantitative phosphoproteomics.

  Kosuke Ogata; Chia-Feng Tsai; Masaki Wakabayashi; Naoyuki Sugiyama; Yasushi Ishihama

  The 64th Annual Conference on Mass Spectrometry, Japan, 18 May 2016

  
• イオンモビリティ分離により加速する高深度ヒトプロテオーム解析

  小形公亮

  日本プロテオーム学会2019年大会（JHUPO 第17回大会）/第70回 日本電気泳動学会総会, 26 Jul. 2019, Invited

  
• キナーゼ基質モチーフ標的型リン酸化プロテオミクス

  小形公亮

  第19回 北里疾患プロテオーム研究会, 16 Mar. 2022, Invited

  
• Digging into Phosphoproteome by Peptide Ion Mobility Separation

  Post-Translational Modifications in Proteomics and Cell Signaling, 10 Mar. 2022, Invited

  
• プロテオミクスLC/MS/MSにおける感度向上を目的とした移動相添加剤の検討

  小形 公亮; Taylor Battellino; Victor Spicer; Oleg Krokhin; 石濱 泰

  第32回クロマトグラフィー科学会議, 26 Nov. 2021

  
• 配列特異的なアミノ酸の相対衝突断面積に基づくペプチドイオンモビリティ予測

  小形公亮; Chih-Hsiang Chang; Darien Yeung; Victor Spicer; Oleg Krokhin; 石濱泰

  第33回バイオメディカル分析科学シンポジウム, 02 Sep. 2021

  
• Proteome-wide profiling of the position specific amino acid contributions to the peptide collision cross-sections

  Kosuke Ogata; Chih-Hsiang Chang; Darien Yeung; Victor Spicer; Oleg Krokhin; Yasushi Ishihama

  PBA2021 31st International Symposium on Pharmaceutical and Biomedical Analysis, 31 Aug. 2021

  
• プロテオミクスイオンモビリティ分離におけるペプチド衝突断面積予測

  小形公亮; Chih-Hsiang Chang; Darien Yeung; Victor Spicer; Oleg Krokhin; 石濱泰

  日本プロテオーム学会2021年大会, 20 Jul. 2021, Invited

  
• 高感度・高スループット プロテオミクスのための要素技術

  小形公亮

  AMR Webinar プロテオミクス最前線, 16 Nov. 2020, Invited

  
• Gradient Refocusing Strategies for Shotgun Proteomics with Meter-Scale Monolithic Silica Capillary Columns

  Kosuke Ogata; Ryota Tomioka; Michio Funahashi; Naoyuki Sugiyama; Yasushi Ishihama

  AOMSC2020, 06 Jan. 2020

  
• メートル長モノリス型シリカカラムとグラジエント再濃縮を用いた高深度プロテオミクス

  小形公亮; 富岡亮太; 舟橋充央; 杉山直幸; 石濱泰

  第30回クロマトグラフィー科学会議, 06 Dec. 2019

  
• Peptide Separation and Quantitation by SRM and PRM: Kinome-Centric Analysis

  Yasushi Ishihama; Kosuke Ogata; Hsin-Yi Chang

  Short course in Frontier Sciences and Technology: Data Analysis in Quantitative Proteomics, 08 Sep. 2019, Invited

  

External funds: Kakenhi

• Spatio-temporal proteomics based on MS silencing

  Grant-in-Aid for Challenging Research (Exploratory)

  Medium-sized Section 47:Pharmaceutical sciences and related fields

  Kyoto University

  Yasushi Ishihama

  From 30 Jul. 2020, To 31 Mar. 2022, Project Closed

  質量分析;プロテオミクス;タンパク質構造;化学修飾;リン酸化修飾

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20K21478/
• Analysis of naturally stealth exosome and its application as drug delivery carrier

  Grant-in-Aid for Scientific Research (B)

  Basic Section 90120:Biomaterials-related

  Kyoto University

  Yuki Takahashi

  From 01 Apr. 2020, To 31 Mar. 2024, Project Closed

  細胞外小胞;エキソソーム;ホスファチジルセリン;血中滞留性

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20H04533/
• Proteomic evaluation of phosphorylation sites regulating molecular interactions based on the analysis of phosphosite stoichiometry

  Grant-in-Aid for Early-Career Scientists

  Basic Section 47020:Pharmaceutical analytical chemistry and physicochemistry-related

  Kyoto University

  小形 公亮

  From 01 Apr. 2025, To 31 Mar. 2027, Granted

  タンパク質リン酸化;プロテオミクス;キナーゼ;質量分析;液体クロマトグラフィー

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-25K18607/

External funds: others

• リン酸化修飾タンパク質構造ダイナミクスの包括的解析

  国立研究開発法人科学技術振興機構, ACT-X 生命現象と機能性物質

  From 01 Oct. 2023, To 31 Mar. 2026
• Host determinants of innate immunity and viral infection under hypoxia

  国立研究開発法人日本医療研究開発機構, 医療分野国際科学技術共同研究開発推進事業

  From 31 Oct. 2022, To 31 Mar. 2023

  研究代表者
• 生体試料中プロテオフォームの一斉計測システムの開発

  中谷医工計測振興財団, 奨励研究助成

  From 01 Apr. 2023, To 31 Mar. 2025

  研究代表者

Education

Teaching subject(s)

• From 01 Apr. 2025, To 31 Mar. 2026

  Fundamental Chemical Experiments

  N308, Fall, Institute for Liberal Arts and Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Advanced Physical Chemistry for Drug Discovery B

  8202, Spring, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2025, To 31 Mar. 2026

  Laboratory Practice in Molecular and Cellular Bioanalysis

  4203, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2025, To 31 Mar. 2026

  Research Proposal Writing Practice B

  8403, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2025, To 31 Mar. 2026

  Research Proposal Writing Practice A

  8402, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2025, To 31 Mar. 2026

  Pharmaceutical Laboratory Coaching Practice A

  8301, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2025, To 31 Mar. 2026

  Advanced Pharmaceutical Sciences II

  6006, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Introduction to Pharmaceutical Sciences

  6002, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Seminar in Molecular and Cellular Bioanalysis

  2303, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Seminar on Critical Reading of Scientific Papers B

  8405, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Seminar on Critical Reading of Scientific Papers A

  8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Introduction to Physical Chemistry for Drug Discovery

  8101, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Introduction to Physical Chemistry for Drug Discovery

  1217, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Advanced Basic Physical Chemistry II

  1212, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Research in Molecular and Cellular Bioanalysis

  3203, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2025, To 31 Mar. 2026

  Medicinal Frontier Science Research C

  8408, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2025, To 31 Mar. 2026

  Medicinal Frontier Science Research B

  8407, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2025, To 31 Mar. 2026

  Medicinal Frontier Science Research A

  8406, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2025, To 31 Mar. 2026

  Pharmaceutical Laboratory I : Analytical and Physical Chemistry

  C901, Spring, Faculty of Pharmaceutical Sciences, 3
• From 01 Apr. 2024, To 31 Mar. 2025

  Research Proposal Writing Practice B

  8403, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2024, To 31 Mar. 2025

  Research Proposal Writing Practice A

  8402, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2024, To 31 Mar. 2025

  Laboratory Practice in Molecular and Cellular Bioanalysis

  4203, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2024, To 31 Mar. 2025

  Laboratory Practice in Molecular and Cellular Bioanalysis

  4203, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2024, To 31 Mar. 2025

  Pharmaceutical Laboratory Coaching Practice A

  8301, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2024, To 31 Mar. 2025

  Advanced Physical Chemistry for Drug Discovery B

  8202, Spring, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2024, To 31 Mar. 2025

  Advanced Physical Chemistry for Drug Discovery A

  8201, Spring, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2024, To 31 Mar. 2025

  Introduction to Physical Chemistry for Drug Discovery

  8101, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Advanced Pharmaceutical Sciences II

  6006, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Introduction to Pharmaceutical Sciences

  6002, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar on Critical Reading of Scientific Papers B

  8405, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar on Critical Reading of Scientific Papers A

  8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Advanced Basic Physical Chemistry II

  1212, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Advanced Basic Physical Chemistry I

  1211, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar in Molecular and Cellular Bioanalysis

  2303, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar in Molecular and Cellular Bioanalysis

  2303, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Introduction to Physical Chemistry for Drug Discovery

  1217, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Pharmaceutical Laboratory I : Analytical and Physical Chemistry

  C901, Spring, Faculty of Pharmaceutical Sciences, 3
• From 01 Apr. 2024, To 31 Mar. 2025

  Medicinal Frontier Science Research C

  8408, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2024, To 31 Mar. 2025

  Research in Molecular and Cellular Bioanalysis

  3203, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2024, To 31 Mar. 2025

  Medicinal Frontier Science Research B

  8407, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2024, To 31 Mar. 2025

  Medicinal Frontier Science Research A

  8406, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2024, To 31 Mar. 2025

  Research in Molecular and Cellular Bioanalysis

  3203, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Research Proposal Writing Practice B

  8403, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2023, To 31 Mar. 2024

  Research Proposal Writing Practice A

  8402, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2023, To 31 Mar. 2024

  Pharmaceutical Laboratory Coaching Practice A

  8301, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2023, To 31 Mar. 2024

  Pharmaceutical Laboratory I : Analytical and Physical Chemistry

  C901, Spring, Faculty of Pharmaceutical Sciences, 3
• From 01 Apr. 2023, To 31 Mar. 2024

  Medicinal Frontier Science Research B

  8407, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Medicinal Frontier Science Research A

  8406, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Pharmaceutical Laboratory 1 : Analytical and Physical Chemistry

  A901, Spring, Faculty of Pharmaceutical Sciences, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Seminar on Critical Reading of Scientific Papers B

  8405, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Seminar on Critical Reading of Scientific Papers A

  8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Pharmaceutical Laboratory Coaching Practice A

  8301, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2022, To 31 Mar. 2023

  Medical Frontier Science Research A

  8406, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Critical Reading of Scientific Papers A

  8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Research Proposal Writing Practice A

  8402, Year-long, Graduate School of Pharmaceutical Sciences, 1

Administration

Faculty management (title, position)

• From 01 Apr. 2024, To 31 Mar. 2025

  情報システム委員会　委員