Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics

Zijuan Lai, Hiroshi Tsugawa, Gert Wohlgemuth, Sajjan Mehta, Matthew Mueller, Yuxuan Zheng, Atsushi Ogiwara, John Meissen, Megan Showalter, Kohei Takeuchi, Tobias Kind, Peter Beal, Masanori Arita, Oliver Fiehn

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives.

Original languageEnglish (US)
Pages (from-to)53-56
Number of pages4
JournalNature Methods
Volume15
Issue number1
DOIs
StatePublished - Jan 3 2018

Fingerprint

Uridine Monophosphate
Metabolome
Metabolites
Gas Chromatography-Mass Spectrometry
Mass spectrometry
Mass Spectrometry
Databases
Gas chromatography
Workflow
Propofol
Liquid Chromatography
Libraries
Software
Liquid chromatography
Deconvolution
Metadata
Enzymes
Derivatives
N-methylalanine

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Lai, Z., Tsugawa, H., Wohlgemuth, G., Mehta, S., Mueller, M., Zheng, Y., ... Fiehn, O. (2018). Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature Methods, 15(1), 53-56. https://doi.org/10.1038/nmeth.4512

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. / Lai, Zijuan; Tsugawa, Hiroshi; Wohlgemuth, Gert; Mehta, Sajjan; Mueller, Matthew; Zheng, Yuxuan; Ogiwara, Atsushi; Meissen, John; Showalter, Megan; Takeuchi, Kohei; Kind, Tobias; Beal, Peter; Arita, Masanori; Fiehn, Oliver.

In: Nature Methods, Vol. 15, No. 1, 03.01.2018, p. 53-56.

Research output: Contribution to journalArticle

Lai, Z, Tsugawa, H, Wohlgemuth, G, Mehta, S, Mueller, M, Zheng, Y, Ogiwara, A, Meissen, J, Showalter, M, Takeuchi, K, Kind, T, Beal, P, Arita, M & Fiehn, O 2018, 'Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics', Nature Methods, vol. 15, no. 1, pp. 53-56. https://doi.org/10.1038/nmeth.4512
Lai, Zijuan ; Tsugawa, Hiroshi ; Wohlgemuth, Gert ; Mehta, Sajjan ; Mueller, Matthew ; Zheng, Yuxuan ; Ogiwara, Atsushi ; Meissen, John ; Showalter, Megan ; Takeuchi, Kohei ; Kind, Tobias ; Beal, Peter ; Arita, Masanori ; Fiehn, Oliver. / Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. In: Nature Methods. 2018 ; Vol. 15, No. 1. pp. 53-56.
@article{2d784c9edd61494aba5500bc8a0071dd,
title = "Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics",
abstract = "Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives.",
author = "Zijuan Lai and Hiroshi Tsugawa and Gert Wohlgemuth and Sajjan Mehta and Matthew Mueller and Yuxuan Zheng and Atsushi Ogiwara and John Meissen and Megan Showalter and Kohei Takeuchi and Tobias Kind and Peter Beal and Masanori Arita and Oliver Fiehn",
year = "2018",
month = "1",
day = "3",
doi = "10.1038/nmeth.4512",
language = "English (US)",
volume = "15",
pages = "53--56",
journal = "PLoS Medicine",
issn = "1549-1277",
publisher = "Nature Publishing Group",
number = "1",

}

TY - JOUR

T1 - Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics

AU - Lai, Zijuan

AU - Tsugawa, Hiroshi

AU - Wohlgemuth, Gert

AU - Mehta, Sajjan

AU - Mueller, Matthew

AU - Zheng, Yuxuan

AU - Ogiwara, Atsushi

AU - Meissen, John

AU - Showalter, Megan

AU - Takeuchi, Kohei

AU - Kind, Tobias

AU - Beal, Peter

AU - Arita, Masanori

AU - Fiehn, Oliver

PY - 2018/1/3

Y1 - 2018/1/3

N2 - Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives.

AB - Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives.

UR - http://www.scopus.com/inward/record.url?scp=85040181528&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85040181528&partnerID=8YFLogxK

U2 - 10.1038/nmeth.4512

DO - 10.1038/nmeth.4512

M3 - Article

AN - SCOPUS:85040181528

VL - 15

SP - 53

EP - 56

JO - PLoS Medicine

JF - PLoS Medicine

SN - 1549-1277

IS - 1

ER -