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Structure Estimation from Metabolite Mass Spectra

Research Project

Project/Area Number 23310143
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied genomics
Research InstitutionThe University of Tokyo

Principal Investigator

ARITA Masanori  東京大学, 理学(系)研究科(研究院), 准教授 (10356389)

Project Period (FY) 2011-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥19,630,000 (Direct Cost: ¥15,100,000、Indirect Cost: ¥4,530,000)
Fiscal Year 2013: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2012: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2011: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Keywordsバイオデータベース / マススペクトル / データベース / フラグメンテーション / GC/MS
Research Abstract

We collected standard mass spectra from GC/MS for primary metabolites from five different research institutions in the world and compared their spectra after consolidating metabolite names and identifiers. Compared results were summarized as a standard library of theoretical spectra. For ESI spectra, we consolidated metabolite names and spectra from multiple repositories such as MassBank, PRIMe, and KNApSAcK. The spectra were compared and merged by considering peak distribution and abundances. In addition, methods for visualizing and comparing chromatograms were also developed. For secondary metabolites, we investigated fragmentation patterns of flavanone, flavone and flavonol and recognized similarity between CID and ESI spectra.
Such results are summarized in our wiki-based data repository. The chromatographic and spectral analyses were realized as a GUI-based software program.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (18 results)

All 2014 2013 2012 2011 Other

All Journal Article (6 results) (of which Peer Reviewed: 4 results) Presentation (9 results) Book (1 results) Remarks (2 results)

  • [Journal Article] Wax ester and lipophilic compound profiling of Euglena gracilis by gas chromatography-mass spectrometry : toward understanding of wax ester fermentation under hypoxia2014

    • Author(s)
      Furuhashi T, Ogawa T, Nakai R, Nakazawa M, Okazawa A, Padermschoke A, Nishio K, Hirai MY, Arita M
    • Journal Title

      Metabolomics

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] MRMPROBS suite for metabolomics using large-scale MRM assays2014

    • Author(s)
      Tsugawa H, Kanazawa M, Ogiwara A, Arita M
    • Journal Title

      Bioinformatics

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Exploration of Polar Lipid Accumulation Profiles in Euglena gracilis Using LipidBlast, a MS/MS Spectral Library Constructed in Silico2014

    • Author(s)
      Ogawa T, Furuhashi T, Okazawa A, Nakai R, Nakazawa M, Kind T, Fiehn O, Kanaya S, Arita M, Ohta D
    • Journal Title

      Bioscience Biotechnology and Biochemistry

      Volume: 78(1)

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
  • [Journal Article] MRMPROBS Suite for metabolomics using large-scale MRM assays2014

    • Author(s)
      Tsugawa H, Kanazawa M, Ogiwara A, Arita M
    • Journal Title

      Bioinformatics

      Volume: accepted

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] MRMPROBS : a data assessment and metabolite identification tool for large-scale multiple reaction monitoring based widely targeted metabolomics2013

    • Author(s)
      Tsugawa H, Arita M, Kanazawa M, Ogiwara A, Bamba T, Fukusaki E
    • Journal Title

      Anal Chem

      Volume: 85(10) Pages: 5191-5199

    • Related Report
      2013 Final Research Report
  • [Journal Article] MRMPROBS: Data Assessment and Metabolite Identification Tool for Large-scale MRM-based Widely Targeted Metabolomics2013

    • Author(s)
      Tsugawa H, Arita M, Kanazawa M, Ogiwara A, Bamba T, Fukusaki E
    • Journal Title

      Analytical Chemistry

      Volume: accepted

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] MassBank and its Future2014

    • Author(s)
      Arita M
    • Organizer
      Cosmos meeting on International Data Exchange in Metabolomics
    • Place of Presentation
      HInxton, Cambridge UK
    • Related Report
      2013 Final Research Report
  • [Presentation] Genetic, Protein, and Metabolic Networks : Which Choice Is Amenable to Modelling2013

    • Author(s)
      Arita M
    • Organizer
      International Conference on Mathematical Modeling and Applications
    • Place of Presentation
      Tokyo, Japan
    • Related Report
      2013 Final Research Report
  • [Presentation] Update on Lipid Databank and other lipidomics initiatives2012

    • Author(s)
      Arita M
    • Organizer
      EMBL-EBI Industry Programme & MetaboLights Project Workshop
    • Place of Presentation
      Hinxton
    • Year and Date
      2012-05-22
    • Related Report
      2013 Final Research Report
  • [Presentation] Cyberinfrastructure for metabolomics and synthetic biology2012

    • Author(s)
      Arita M
    • Organizer
      International Symposium on Biotechnology for Green Growth
    • Place of Presentation
      Kobe, Japan
    • Related Report
      2013 Final Research Report
  • [Presentation] What can metabolomics learn from genomics and proteomics?2012

    • Author(s)
      Arita M
    • Organizer
      International Conference of Research and Application on Traditional Complementary and Alternative Medicine (TCAM)
    • Place of Presentation
      Muhammadiyah University of Surakarta (Indonesia)
    • Related Report
      2013 Final Research Report
  • [Presentation] Wiki-based Databases : Integration of knowledge through the web2011

    • Author(s)
      Arita M
    • Organizer
      C-NAIR Seminar Nasional
    • Place of Presentation
      Gadjah Mada University (Indonesia)
    • Year and Date
      2011-12-05
    • Related Report
      2013 Final Research Report
  • [Presentation] Wiki-based Databases : Integration of knowledge through the web2011

    • Author(s)
      Arita M
    • Organizer
      C-NAIR Seminar National
    • Place of Presentation
      Gadjah Mada University, Jogjakarta, Indonesia(招待講演)
    • Year and Date
      2011-12-05
    • Related Report
      2011 Annual Research Report
  • [Presentation] Knowledge Management using a Wiki-based System and its Application to Mass Spectra2011

    • Author(s)
      Arita M
    • Organizer
      EBI Seminar
    • Place of Presentation
      European Bioinformatics Institute, Hinxton, UK(招待講演)
    • Year and Date
      2011-04-19
    • Related Report
      2011 Annual Research Report
  • [Presentation] Assessing Theoretical Spectra for Flavonoids using MassBank

    • Author(s)
      Arita M
    • Organizer
      ICP2014
    • Related Report
      2013 Final Research Report
  • [Book] 「使えるデータベース・ウェブツール」実験医学別冊2011

    • Author(s)
      有田正規
    • Total Pages
      29
    • Publisher
      羊土社
    • Related Report
      2013 Final Research Report
  • [Remarks] 研究成果はhttp://metabolomics.jp/ および現在も作成を継続中のマススペクトルデータベース上に掲載予定.標準品のスペクトルデータおよびそのアノテーションは MassBankデータベースに掲載.

    • Related Report
      2013 Final Research Report
  • [Remarks]

    • URL

      http://metabolomics.jp/

    • Related Report
      2011 Annual Research Report

URL: 

Published: 2011-04-06   Modified: 2019-07-29  

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