Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices
Review article, 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.
Author
Saleh Alseekh
Max Planck Society
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 University Jena
Jennifer C. Ewald
University of Tübingen
Paul D. Fraser
Royal Holloway University of London
Patrick Giavalisco
Max Planck Society
Robert D. Hall
Wageningen University and Research
Matthias Heinemann
University of Groningen
Hannes Link
Max Planck Institute for Terrestrial Microbiology
Jie Luo
Hainan University
Steffen Neumann
Leibniz Institute for Plant Biochemistry
Jens B Nielsen
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
BioInnovation Institute
Leonardo Perez de Souza
Max Planck Society
Kazuki Saito
RIKEN
Chiba University
Uwe Sauer
Swiss Federal Institute of Technology in Zürich (ETH)
Frank C. Schroeder
Cornell University
Stefan Schuster
Friedrich Schiller University Jena
Gary Siuzdak
Scripps Research Institute
Aleksandra Skirycz
Cornell University
Max Planck Society
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
Swiss Federal Institute of Technology in Zürich (ETH)
Alisdair R. Fernie
Max Planck Society
Institute of Plants Systems Biology and Biotechnology
Nature Methods
1548-7091 (ISSN) 1548-7105 (eISSN)
Vol. 18 7 747-756Subject Categories
Cell Biology
Analytical Chemistry
DOI
10.1038/s41592-021-01197-1
PubMed
34239102