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Kosuke Ogata

Graduate School of Pharmaceutical Sciences, Division of Bioinformatics and Chemical Genomics Assistant Professor

Kosuke Ogata
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    Last Updated :2022/05/14

    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)

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      Last Updated :2022/05/14

      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
      • 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

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