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

doi:10.1038/s41592-019-0358-2

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

228 Citations (Scopus)

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 language	English
Pages (from-to)	295-298
Journal	Nature Methods
Volume	16
Issue number	4
DOIs	https://doi.org/10.1038/s41592-019-0358-2
Publication status	Published - 28 Mar 2019

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10.1038/s41592-019-0358-2

EPPN: European Plant Phenotyping Network
1/01/12 → 31/12/15
Project: EU research project
NUE-CROPS: Improving nutrient efficiency in major European food, feed and biofuel crops to reduce the negative environmental impact of crop production
1/05/09 → 30/04/14
Project: EU research project

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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, J. A., Oztolan-Erol, N., Keurentjes, J. J. B., Arita, M., & 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

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title = "A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms",

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. ",

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

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doi = "10.1038/s41592-019-0358-2",

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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

TY - JOUR

T1 - A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms

AU - Tsugawa, Hiroshi

AU - Nakabayashi, Ryo

AU - Mori, Tetsuya

AU - Yamada, Yutaka

AU - Takahashi, Mikiko

AU - Rai, Amit

AU - Sugiyama, Ryosuke

AU - Yamamoto, Hiroyuki

AU - Nakaya, Taiki

AU - Yamazaki, Mami

AU - Kooke, Rik

AU - Bac-Molenaar, Johanna A.

AU - Oztolan-Erol, Nihal

AU - Keurentjes, Joost J.B.

AU - Arita, Masanori

AU - Saito, Kazuki

PY - 2019/3/28

Y1 - 2019/3/28

N2 - 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.

AB - 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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DO - 10.1038/s41592-019-0358-2

M3 - Article

C2 - 30923379

AN - SCOPUS:85063618251

SN - 1548-7091

VL - 16

SP - 295

EP - 298

JO - Nature Methods

JF - Nature Methods

IS - 4

ER -

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

Abstract

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Projects

EPPN: European Plant Phenotyping Network

NUE-CROPS: Improving nutrient efficiency in major European food, feed and biofuel crops to reduce the negative environmental impact of crop production

Cite this