Centers & Labs

RIKEN Center for Sustainable Resource Science

Metabolome Informatics Research Team

Team Leader: Masanori Arita (D.Sci.)
Masanori  Arita(D.Sci.)

Our team develops software platforms necessary for metabolomic analyses, network analyses and computer simulations. We also design databases that help more efficient identification of metabolites. The developed software will be applied to integrated analysis of metabolomic and transcriptomic data collated by other teams to enable systematic understanding of plants.

Main Research Field

Complex systems

Related Research Fields

Biological Sciences

Keywords

  • Genome
  • Database
  • Metabolome
  • Algorithm

Selected Publications

  1. Tsugawa H, Ikeda K, Tanaka W, Senoo Y, Arita M, Arita M
    "Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library"
    Journal of Cheminformatics 9:19, 2017
  2. Wohlgemuth G, Mehta SS, Mejia RF, Neumann S, Pedrosa D, Pluskal T, Schymanski EL, Willighagen EL, Wilson M, Wishart DS, Arita M, Dorrestein PC, Bandeira N, Wang M, Schulze T, Salek RM, Steinbeck C, Nainala VC, Mistrik R, Nishioka T, Fiehn O
    "SPLASH, a hashed identifier for mass spectra"
    Nature Biotechnology 34(11):1099-1101, 2016
  3. Tsugawa H, Kind T, Nakabayashi R, Yukihira D, Tanaka W, Cajka T, Saito K, Fiehn O, Arita M.
    "Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software"
    Analytical Chemistry 88(16):7946-7958, 2016
  4. Fukushima A, Nakamura M, Suzuki H, Yamazaki M, Knoch E, Mori T, Umemoto N, Morita M, Hirai G, Sodeoka M, Saito K
    "Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling"
    Frontiers in Plant Science 7:1883, 2016
  5. Tsugawa H, Cajka T, Kind T, Ma Y, Higgins B, Ikeda K, Kanazawa M, VanderGheynst J, Fiehn O, Arita M:
    "MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis"
    Nature Methods 12(6), 523-526, 2015
  6. Fukushima A, Nakamura M, Suzuki H, Saito K, Yamazaki M:
    "High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome"
    PLOS One 10(6), e0129154, 2015
  7. Hasegawa Y, Arita M:
    "Optimal implementations for reliable circadian clocks"
    Physical Review Letters 113(10), 108101, 2014
  8. Fukushima A, Kusano M.:
    "Recent progress in the development of metabolome databases for plant systems biology"
    Frontiers in Plant Science, 4(73), 2013
  9. Fukushima A.:
    "DiffCorr: an R package to analyze and visualize differential correlations in biological networks"
    Gene, 518(1), 209-214, 2013
  10. Tsugawa H, Arita M, Kanazawa M, Ogiwara A, Bamba T, Fukusaki E.:
    "MRMPROBS: a data assessment and metabolite identification tool for large-scale multiple reaction monitoring based widely targeted metabolomics"
    Anal Chem, 85(10), 5191-5199, 2013

Lab Members

Principal Investigator

Masanori Arita
Team Leader

Core Members

Atsushi Fukushima
Research Scientist
Hiroshi Tsugawa
Research Scientist

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan

Email: Masanori.arita [at] riken.jp

Related links