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

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

in Annotations / Best practice / Chromatography / Complexity / Gas chromatography / Guidelines / Ion recombination / Ions / Isomers / Liquid chromatography / Mass spectrometry / Mass spectroscopy / Metabolites / Metabolomics / Recombination / Sample preparation / Scientific imaging / Spectroscopy

2021

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2021

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Journal Article

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

D’Auria John,

Fraser, Paul D,

Tohge Takayuki,

Giavalisco, Patrick,

Hall, Robert D,

Skirycz Aleksandra,

Nielsen, Jens,

Wu, Si,

Schroeder, Frank C,

Wen Weiwei,

Aharoni Asaph,

Brotman Yariv,

Perez de Souza Leonardo,

Fernie, Alisdair R,

Xu Guowang,

Contrepois Kévin,

Neumann Steffen,

C Ewald Jennifer,

Snyder, Michael P,

Saleh, Alseekh,

Heinemann, Matthias,

Saito Kazuki,

Siuzdak Gary,

Wang, Yulan,

Ewald, Jan,

Zamboni, Nicola,

Luo, Jie,

Link Hannes,

Tang Huiru,

Sauer, Uwe,

Sumner, Lloyd W,

Schuster, Stefan

2021

Overview

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.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.

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Nature Publishing Group

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