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

Saleh Alseekh, Asaph Aharoni, Yariv Brotman, Kévin 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 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

Research output: Contribution to journalReview articlepeer-review

419 Scopus citations


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 languageEnglish
Pages (from-to)747-756
Number of pages10
JournalNature Methods
Issue number7
StatePublished - 1 Jul 2021

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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