Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices
Reviewartikel, 2021

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.


Saleh Alseekh


Institute of Plants Systems Biology and Biotechnology

Asaph Aharoni

Weizmann Institute of Science

Yariv Brotman

Ben-Gurion University of the Negev

Kevin Contrepois

Stanford University

John D'Auria

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

Jan Ewald

Friedrich-Schiller-Universität Jena

Jennifer C. Ewald

Universität Tübingen

Paul D. Fraser

Royal Holloway University of London

Patrick Giavalisco


Robert D. Hall

Wageningen University and Research

Matthias Heinemann

Rijksuniversiteit Groningen

Hannes Link

Max Planck Institute for Terrestrial Microbiology

Jie Luo

Hainan University

Steffen Neumann

Leibniz Institut fur Pflanzenbiochemie

Jens B Nielsen

Chalmers, Biologi och bioteknik, Systembiologi

BioInnovation Institute

Leonardo Perez de Souza


Kazuki Saito


Chiba University

Uwe Sauer

Eidgenössische Technische Hochschule Zürich (ETH)

Frank C. Schroeder

Cornell University

Stefan Schuster

Friedrich-Schiller-Universität Jena

Gary Siuzdak

Scripps Research Institute

Aleksandra Skirycz

Cornell University


Lloyd W. Sumner

University of Missouri

Michael P. Snyder

Stanford University

Huiru Tang

Fudan University

Takayuki Tohge

Nara Institute of Science and Technology

Yulan Wang

Nanyang Technological University

Weiwei Wen

Huazhong Agricultural University

Si Wu

Stanford University

Guowang Xu

Chinese Academy of Sciences

Nicola Zamboni

Eidgenössische Technische Hochschule Zürich (ETH)

Alisdair R. Fernie


Institute of Plants Systems Biology and Biotechnology

Nature Methods

1548-7091 (ISSN) 1548-7105 (eISSN)

Vol. 18 7 747-756



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