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Development of a comprehensive splice-site analysis using mass spectrometry-based proteomics

Research Project

Project/Area Number 20500271
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionHiroshima University

Principal Investigator

ISHINO Yoko  Hiroshima University, 産学・地域連携センター, 研究員 (90373266)

Project Period (FY) 2008 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2009: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2008: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywordsプロテオーム情報処理 / 機械学習 / バイオインフォマティクス
Research Abstract

This study aimed to establish a method of accurately and comprehensively detecting the splice donor and acceptor sites of alternative splicing. The method is based on a de novo sequencing method, which directly identifies partial amino acid sequences of expressed proteins from the mass spectrometry-based proteome data. In addition, predicting the ease of peptide detection in proteomics using theoretical physicochemical properties of peptides is newly incorporated into the method in order to improve the accuracy of the splice site detection. Although the proposed method was evaluated with proteomics experimental data, it produced poor results. However, this led to the study of improving the mass accuracy of the mass spectrometry-based proteome data. A computational a posteriori calibration method was newly proposed, and based on the proteome data of fission yeast it was confirmed that the developed method increased mass accuracy.

Report

(4 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (20 results)

All 2011 2010 2009 2008

All Journal Article (8 results) (of which Peer Reviewed: 8 results) Presentation (12 results)

  • [Journal Article] In Silico 3D Structure Prediction of Activated GPCRs as a Drug Target2011

    • Author(s)
      石野洋子, 原田隆範
    • Journal Title

      Proceedings of the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics

      Pages: 261-265

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] In Silico 3D Structure Prediction of Activated GPCRs as a Drug Target2011

    • Author(s)
      Yoko Ishino, Takanori Harada
    • Journal Title

      Proc.of the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics

      Pages: 261-265

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dead time loss correction of mass errors occurring in high-throughput proteomics based on electrospray ionization time-of-flight tandem mass spectrometry2010

    • Author(s)
      Yoko Ishino, Hisaaki Taniguchi
    • Journal Title

      Rapid Communications in Mass Spectrometry Vol.24

      Pages: 1490-1495

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Dead time loss correction of mass errors occurring in high-throughput proteomics based on electrospray ionization time-of-flight tandem mass spectrometry2010

    • Author(s)
      Y.Ishino, H.Taniguchi
    • Journal Title

      Rapid Communications in Mass Spectrometry (in press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 実数値GAを用いた薬物標的GPCRの活性型立体構造の探索2009

    • Author(s)
      石野洋子, 原田隆範, 相田美砂子
    • Journal Title

      人工知能学会論文誌 Vol.24

      Pages: 386-396

    • NAID

      130000137873

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] プロテオミクスによるタンパク質リン酸化の解析2009

    • Author(s)
      山内英美子, 石野洋子, 小西博昭
    • Journal Title

      生体の科学 Vol.60

      Pages: 151-157

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] 実数値GAを用いた薬物標的GPCRの活性型立体構造の探索2009

    • Author(s)
      石野洋子, 原田隆範, 相田美砂子
    • Journal Title

      人工知能学会論文誌 24

      Pages: 386-396

    • NAID

      130000137873

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] プロテオミクスによるタンパク質リン酸化の解析2009

    • Author(s)
      山内英美子, 石野洋子, 小西博昭
    • Journal Title

      生体の科学 (印刷中)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] In Silico 3D Structure Prediction of Activated GPCRs as a Drug Target2011

    • Author(s)
      Yoko Ishino, Takanori Harada
    • Organizer
      the 2011 International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB2011)
    • Place of Presentation
      Peninsula Excelsior Hotel, Singapore
    • Related Report
      2010 Final Research Report
  • [Presentation] An Accurate Mass Error Correction Method in LC-MS/MS Proteome Analysis2011

    • Author(s)
      Yoko Ishino, Hisaaki Taniguchi
    • Organizer
      the 9th Asia Pacific Bioinformatics Conference (APBC2011)
    • Place of Presentation
      Incheon, Korea
    • Related Report
      2010 Final Research Report
  • [Presentation] In Silico 3D Structure Prediction of Activated GPCRs as a Drug Target2011

    • Author(s)
      Yoko Ishino, Takanori Harada
    • Organizer
      2011 International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB2011)
    • Place of Presentation
      Singapore
    • Related Report
      2010 Annual Research Report
  • [Presentation] An Accurate Mass Error Correction Method in LC-MS/MS Proteome Analysis2011

    • Author(s)
      Yoko Ishino, Hisaaki Taniguchi
    • Organizer
      The 9^<th> Asia Pacific Bioinformatics Conference (APBC2011)
    • Place of Presentation
      Incheon, Korea
    • Related Report
      2010 Annual Research Report
  • [Presentation] A Posteriori Calibration Method for Genome-Wide Proteomics Using LC/ESI-TOF MS/MS2010

    • Author(s)
      Yoko Ishino, Hisaaki Taniguchi
    • Organizer
      the 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
    • Place of Presentation
      Fukuoka, Japan
    • Related Report
      2010 Final Research Report
  • [Presentation] A Posteriori Calibration Method for Genome-Wide Proteomics Using LC/ESI-TOF MS/MS2010

    • Author(s)
      Yoko Ishino, Hisaaki Taniguchi
    • Organizer
      The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
    • Place of Presentation
      Fukuoka, Japan
    • Related Report
      2010 Annual Research Report
  • [Presentation] Prediction of Eukaryotic Translation Initiation Sites Using Machine Learning2009

    • Author(s)
      Yoko Ishino
    • Organizer
      the 20th International Conference on Genome Informatics (GIW2009)
    • Place of Presentation
      Yokohama, Japan
    • Related Report
      2010 Final Research Report
  • [Presentation] Search for 3D Structure of Drug Target GPCR Active Forms, BioInfo20092009

    • Author(s)
      Yoko Ishino, Takanori Harada, Misako Aida
    • Organizer
      CBI (the Chem-Bio Informatics Society) and KSBSB (the Korean Society for Bioinformatics) Joint Conference
    • Place of Presentation
      Busan, Korea
    • Related Report
      2010 Final Research Report
  • [Presentation] Prediction of Eukaryotic Translation Initiation Sites Using Machine Learning2009

    • Author(s)
      Yoko Ishino
    • Organizer
      the 20^<th> International Conference on Genome Informatics (GIW2009)
    • Place of Presentation
      Yokohama, Japan
    • Related Report
      2009 Annual Research Report
  • [Presentation] Search for 3D Structure of Drug Target GPCR Active Forms2009

    • Author(s)
      Yoko Ishino, Takanori Harada, Misako Aida
    • Organizer
      Biolnfo2009, CBI (the Chem-Bio Informatics Society) and KSBSB (the Korean Society for Bioinformatics) Joint Conference
    • Place of Presentation
      Busan, Korea
    • Related Report
      2009 Annual Research Report
  • [Presentation] Conformation Search of Drug Target GPCR Using Real-Coded Genetic Algorithm2008

    • Author(s)
      Yoko Ishino, Takanori Harada, Misako Aida
    • Organizer
      The 2008 Annual Conference of the Japanese Society for Bioinformatics
    • Place of Presentation
      Senri Life Science Center, Osaka, Japan
    • Year and Date
      2008-12-16
    • Related Report
      2008 Annual Research Report
  • [Presentation] Conformation Search of Drug Target GPCR Using Real-Coded Genetic Algorithm2008

    • Author(s)
      Yoko Ishino, Takanori Harada, Misako Aida
    • Organizer
      the 2008 Annual Conference of the Japanese Society for Bioinformatics
    • Place of Presentation
      Osaka, Japan
    • Related Report
      2010 Final Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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