Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Saleh Alseekh; Asaph Aharoni; Yariv Brotman; Kevin Contrepois; John D'Auria; Jan Ewald; Jennifer C Ewald; Paul D Fraser; Patrick Giavalisco; Robert D Hall; Matthias Heinemann; Hannes Link; Jie Luo; Steffen Neumann; Jens B Nielsen; Leonardo Perez de Souza; Kazuki Saito; Uwe Sauer; Frank C Schroeder; Stefan Schuster; Gary Siuzdak; Aleksandra Skirycz; Lloyd W Sumner; Michael P Snyder; Huiru Tang; Takayuki Tohge; Yulan Wang; Weiwei Wen; Si Wu; Guowang Xu; Nicola Zamboni; Alisdair R Fernie

doi:10.1038/s41592-021-01197-1

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Saleh Alseekh, Asaph Aharoni, Yariv Brotman, Kevin Contrepois, John D'Auria, Jan Ewald, Jennifer C Ewald, Paul D Fraser, Patrick Giavalisco, Robert D Hall, Matthias Heinemann, Hannes Link, Jie Luo, Steffen Neumann, Jens B Nielsen, Leonardo Perez de Souza, Kazuki Saito, Uwe Sauer, Frank C Schroeder, Stefan SchusterGary Siuzdak, Aleksandra Skirycz, Lloyd W Sumner, Michael P Snyder, Huiru Tang, Takayuki Tohge, Yulan Wang, Weiwei Wen, Si Wu, Guowang Xu, Nicola Zamboni, Alisdair R Fernie^*

^*Corresponding author for this work

Department of Plant and Environmental Sciences

Research output: Contribution to journal › Review article › peer-review

474 Citations (Scopus)

Abstract

This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics. Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.

Original language	English
Pages (from-to)	747-756
Number of pages	10
Journal	Nature Methods
Volume	18
Issue number	7
DOIs	https://doi.org/10.1038/s41592-021-01197-1
Publication status	Published - 8 Jul 2021

All Science Journal Classification (ASJC) codes

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Alseekh, S., Aharoni, A., Brotman, Y., Contrepois, K., D'Auria, J., Ewald, J., Ewald, J. C., Fraser, P. D., Giavalisco, P., Hall, R. D., Heinemann, M., Link, H., Luo, J., Neumann, S., Nielsen, J. B., de Souza, L. P., Saito, K., Sauer, U., Schroeder, F. C., ... Fernie, A. R. (2021). Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Nature Methods, 18(7), 747-756. https://doi.org/10.1038/s41592-021-01197-1

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title = "Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices",

abstract = "This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics. Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.",

author = "Saleh Alseekh and Asaph Aharoni and Yariv Brotman and Kevin Contrepois and John D'Auria and Jan Ewald and Ewald, {Jennifer C} and Fraser, {Paul D} and Patrick Giavalisco and Hall, {Robert D} and Matthias Heinemann and Hannes Link and Jie Luo and Steffen Neumann and Nielsen, {Jens B} and {de Souza}, {Leonardo Perez} and Kazuki Saito and Uwe Sauer and Schroeder, {Frank C} and Stefan Schuster and Gary Siuzdak and Aleksandra Skirycz and Sumner, {Lloyd W} and Snyder, {Michael P} and Huiru Tang and Takayuki Tohge and Yulan Wang and Weiwei Wen and Si Wu and Guowang Xu and Nicola Zamboni and Fernie, {Alisdair R}",

year = "2021",

month = jul,

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doi = "10.1038/s41592-021-01197-1",

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Alseekh, S, Aharoni, A, Brotman, Y, Contrepois, K, D'Auria, J, Ewald, J, Ewald, JC, Fraser, PD, Giavalisco, P, Hall, RD, Heinemann, M, Link, H, Luo, J, Neumann, S, Nielsen, JB, de Souza, LP, Saito, K, Sauer, U, Schroeder, FC, Schuster, S, Siuzdak, G, Skirycz, A, Sumner, LW, Snyder, MP, Tang, H, Tohge, T, Wang, Y, Wen, W, Wu, S, Xu, G, Zamboni, N & Fernie, AR 2021, 'Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices', Nature Methods, vol. 18, no. 7, pp. 747-756. https://doi.org/10.1038/s41592-021-01197-1

TY - JOUR

T1 - Mass spectrometry-based metabolomics

T2 - a guide for annotation, quantification and best reporting practices

AU - Alseekh, Saleh

AU - Aharoni, Asaph

AU - Brotman, Yariv

AU - Contrepois, Kevin

AU - D'Auria, John

AU - Ewald, Jan

AU - Ewald, Jennifer C

AU - Fraser, Paul D

AU - Giavalisco, Patrick

AU - Hall, Robert D

AU - Heinemann, Matthias

AU - Link, Hannes

AU - Luo, Jie

AU - Neumann, Steffen

AU - Nielsen, Jens B

AU - de Souza, Leonardo Perez

AU - Saito, Kazuki

AU - Sauer, Uwe

AU - Schroeder, Frank C

AU - Schuster, Stefan

AU - Siuzdak, Gary

AU - Skirycz, Aleksandra

AU - Sumner, Lloyd W

AU - Snyder, Michael P

AU - Tang, Huiru

AU - Tohge, Takayuki

AU - Wang, Yulan

AU - Wen, Weiwei

AU - Wu, Si

AU - Xu, Guowang

AU - Zamboni, Nicola

AU - Fernie, Alisdair R

PY - 2021/7/8

Y1 - 2021/7/8

N2 - This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics. Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.

AB - This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics. Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.

UR - http://www.scopus.com/inward/record.url?scp=85109787667&partnerID=8YFLogxK

U2 - 10.1038/s41592-021-01197-1

DO - 10.1038/s41592-021-01197-1

M3 - Review article

C2 - 34239102

SN - 1548-7091

VL - 18

SP - 747

EP - 756

JO - Nature Methods

JF - Nature Methods

IS - 7

ER -

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Abstract

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