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MassBank: a public repository for sharing mass spectral data for life sciences

  1. Hisayuki Horai1,
  2. Masanori Arita1,2,3,†,
  3. Shigehiko Kanaya4,
  4. Yoshito Nihei1,
  5. Tasuku Ikeda1,
  6. Kazuhiro Suwa2,
  7. Yuya Ojima1,
  8. Kenichi Tanaka4,
  9. Satoshi Tanaka5,6,
  10. Ken Aoshima5,6,
  11. Yoshiya Oda5,6,
  12. Yuji Kakazu1,
  13. Miyako Kusano3,
  14. Takayuki Tohge3,
  15. Fumio Matsuda3,
  16. Yuji Sawada3,6,
  17. Masami Yokota Hirai3,6,
  18. Hiroki Nakanishi6,7,
  19. Kazutaka Ikeda6,7,
  20. Naoshige Akimoto8,
  21. Takashi Maoka9,
  22. Hiroki Takahashi4,
  23. Takeshi Ara10,
  24. Nozomu Sakurai10,
  25. Hideyuki Suzuki10,
  26. Daisuke Shibata10,
  27. Steffen Neumann11,
  28. Takashi Iida12,
  29. Ken Tanaka13,
  30. Kimito Funatsu14,
  31. Fumito Matsuura15,
  32. Tomoyoshi Soga1,
  33. Ryo Taguchi6,7,
  34. Kazuki Saito3,
  35. Takaaki Nishioka1,*

Article first published online: 7 JUL 2010

DOI: 10.1002/jms.1777

Issue

Journal of Mass Spectrometry

Journal of Mass Spectrometry

Volume 45, Issue 7, pages 703–714, July 2010

Additional Information

How to Cite

Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., Oda, Y., Kakazu, Y., Kusano, M., Tohge, T., Matsuda, F., Sawada, Y., Hirai, M. Y., Nakanishi, H., Ikeda, K., Akimoto, N., Maoka, T., Takahashi, H., Ara, T., Sakurai, N., Suzuki, H., Shibata, D., Neumann, S., Iida, T., Tanaka, K., Funatsu, K., Matsuura, F., Soga, T., Taguchi, R., Saito, K. and Nishioka, T. (2010), MassBank: a public repository for sharing mass spectral data for life sciences. Journal of Mass Spectrometry, 45: 703–714. doi: 10.1002/jms.1777

Author Information

  1. 1

    Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan

  2. 2

    Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan

  3. 3

    RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan

  4. 4

    Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan

  5. 5

    Biomarkers and Personalized Medicine Core Function Unit, Eisai Product Creation Systems, Eisai Co. Ltd, Tsukuba, Ibaraki 300-2635, Japan

  6. 6

    JST, CREST, Kawaguchi, Saitama 332-0012, Japan

  7. 7

    Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan

  8. 8

    Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan

  9. 9

    Research Institute for Production Development, Kyoto 606-0805, Japan

  10. 10

    Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan

  11. 11

    Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, 06120 Halle, Germany

  12. 12

    College of Humanities and Sciences, Nihon University, Tokyo 156-8550, Japan

  13. 13

    Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan

  14. 14

    Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan

  15. 15

    Faculty of Life Science and Biotechnology, Fukuyama University, Fukuyama, Hiroshima 729-0292, Japan

  1. †

    Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.

*Institute for Advanced Biosciences, Keio University, 14-1 Banba-cho, Tsuruoka, Yamagata 997-0035, Japan.

Publication History

  1. Issue published online: 8 JUL 2010
  2. Article first published online: 7 JUL 2010
  3. Manuscript Accepted: 1 JUN 2010
  4. Manuscript Received: 18 MAR 2010

Funded by

  • Institute for Bioinformatics Research
  • Development of the Japan Science and Technology Agency
  • Priority Area from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Grant Number: 18016028
  • New Energy and Industrial Technology Development Organization (NEDO)

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Keywords:

  • MassBank;
  • public database;
  • distributed database;
  • metabolite;
  • spectral similarity

Abstract

MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron-ionization mass spectrometry(EI-MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)-MSn data of 2337 authentic compounds of metabolites, 11 545 EI-MS and 834 other-MS data of 10 286 volatile natural and synthetic compounds, and 3045 ESI-MS2 data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI-MS2 data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass-to-charge ratio are optimized to the ESI-MS2 data. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI-MS2 data on an identical compound under different collision-induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21–23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data. Copyright © 2010 John Wiley & Sons, Ltd.

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