Basic Information

Faculty

• Faculty of Pharmaceutical Sciences

Academic Degree

• 23 Mar. 2022

  京都大学博士（薬学）
• 修士（薬科学）(京都大学)

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

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

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

  Cell Reports Methods, 24 Jan. 2022, Lead author

  
• 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

  
• 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

  
• 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

  
• 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, 30 Jan. 2021, Peer-reviewed, Lead author

  
• 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

  
• 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

  
• 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.

• 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

  
• 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

  
• シグナル伝達経路解明に向けた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; Chia-Feng Tsai; 杉山直幸; 石濱泰

  第44回日本分子生物学会年会, 01 Dec. 2021

  

Presentations

• 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

  石濱 泰

  From 30 Jul. 2020, To 31 Mar. 2022, Granted

  質量分析;プロテオミクス;タンパク質構造;化学修飾

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20K21478/
• 天然ステルスエキソソームの解析とデリバリーキャリア開発への応用

  Grant-in-Aid for Scientific Research (B)

  Basic Section 90120:Biomaterials-related

  Kyoto University

  高橋 有己

  From 01 Apr. 2020, To 31 Mar. 2024, Granted

  エキソソーム;血中滞留性

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20H04533/