A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms

Hiroshi Tsugawa, Ryo Nakabayashi, Tetsuya Mori, Yutaka Yamada, Mikiko Takahashi, Amit Rai, Ryosuke Sugiyama, Hiroyuki Yamamoto, Taiki Nakaya, Mami Yamazaki, Rik Kooke, Johanna A. Bac-Molenaar, Nihal Oztolan-Erol, Joost J.B. Keurentjes, Masanori Arita, Kazuki Saito

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Abstract

We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc.riken.jp/) for metabolite structure characterization using fully 13 C-labeled and non-labeled plants and LC–MS/MS. Our approach facilitates carbon number determination and metabolite classification for unknown molecules. Applying our method to 31 tissues from 12 plant species, we assigned 1,092 structures and 344 formulae to 3,604 carbon-determined metabolite ions, 69 of which were found to represent structures currently not listed in metabolome databases.

Original languageEnglish
Pages (from-to)295-298
JournalNature Methods
Volume16
Issue number4
DOIs
Publication statusPublished - 28 Mar 2019

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Metabolome
Metabolites
Isotopes
Carbon
Databases
Ions
Tissue
Molecules

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Tsugawa, H., Nakabayashi, R., Mori, T., Yamada, Y., Takahashi, M., Rai, A., ... Saito, K. (2019). A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. Nature Methods, 16(4), 295-298. https://doi.org/10.1038/s41592-019-0358-2
Tsugawa, Hiroshi ; Nakabayashi, Ryo ; Mori, Tetsuya ; Yamada, Yutaka ; Takahashi, Mikiko ; Rai, Amit ; Sugiyama, Ryosuke ; Yamamoto, Hiroyuki ; Nakaya, Taiki ; Yamazaki, Mami ; Kooke, Rik ; Bac-Molenaar, Johanna A. ; Oztolan-Erol, Nihal ; Keurentjes, Joost J.B. ; Arita, Masanori ; Saito, Kazuki. / A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. In: Nature Methods. 2019 ; Vol. 16, No. 4. pp. 295-298.
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abstract = "We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc.riken.jp/) for metabolite structure characterization using fully 13 C-labeled and non-labeled plants and LC–MS/MS. Our approach facilitates carbon number determination and metabolite classification for unknown molecules. Applying our method to 31 tissues from 12 plant species, we assigned 1,092 structures and 344 formulae to 3,604 carbon-determined metabolite ions, 69 of which were found to represent structures currently not listed in metabolome databases.",
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Tsugawa, H, Nakabayashi, R, Mori, T, Yamada, Y, Takahashi, M, Rai, A, Sugiyama, R, Yamamoto, H, Nakaya, T, Yamazaki, M, Kooke, R, Bac-Molenaar, JA, Oztolan-Erol, N, Keurentjes, JJB, Arita, M & Saito, K 2019, 'A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms' Nature Methods, vol. 16, no. 4, pp. 295-298. https://doi.org/10.1038/s41592-019-0358-2

A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. / Tsugawa, Hiroshi; Nakabayashi, Ryo; Mori, Tetsuya; Yamada, Yutaka; Takahashi, Mikiko; Rai, Amit; Sugiyama, Ryosuke; Yamamoto, Hiroyuki; Nakaya, Taiki; Yamazaki, Mami; Kooke, Rik; Bac-Molenaar, Johanna A.; Oztolan-Erol, Nihal; Keurentjes, Joost J.B.; Arita, Masanori; Saito, Kazuki.

In: Nature Methods, Vol. 16, No. 4, 28.03.2019, p. 295-298.

Research output: Contribution to journalArticleAcademicpeer-review

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Tsugawa H, Nakabayashi R, Mori T, Yamada Y, Takahashi M, Rai A et al. A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. Nature Methods. 2019 Mar 28;16(4):295-298. https://doi.org/10.1038/s41592-019-0358-2