Mass Spectrometry-based Metabolomics: a Guide for Annotation, Quantification and Best Reporting Practices

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2021 Jul 9

PMID 34239102

Citations 280

Authors

Saleh Alseekh

Asaph Aharoni

Yariv Brotman

Kevin Contrepois

John DAuria

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 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

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Critical assessment of quenching and extraction/sample preparation methods for microorganisms in metabolomics.

Sedighikamal H, Mashayekhan S Metabolomics. 2025; 21(2):40.

PMID: 40082321 DOI: 10.1007/s11306-025-02228-0.

Advancements in proteogenomics for preclinical targeted cancer therapy research.

Suo Y, Song Y, Wang Y, Liu Q, Rodriguez H, Zhou H Biophys Rep. 2025; 11(1):56-76.

PMID: 40070661 PMC: 11891078. DOI: 10.52601/bpr.2024.240053.

Plant metabolomics: applications and challenges in the era of multi-omics big data.

Hao Y, Zhang Z, Luo E, Yang J, Wang S aBIOTECH. 2025; 6(1):116-132.

PMID: 40060186 PMC: 11889285. DOI: 10.1007/s42994-024-00194-0.

Tandem metabolic reaction-based sensors unlock in vivo metabolomics.

Cheng X, Li Z, Zhu J, Wang J, Huang R, Yu L Proc Natl Acad Sci U S A. 2025; 122(9):e2425526122.

PMID: 40014569 PMC: 11892595. DOI: 10.1073/pnas.2425526122.

Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.

Fan B, Chen L, Chen L, Guo H Int J Mol Sci. 2025; 26(4).

PMID: 40003933 PMC: 11855028. DOI: 10.3390/ijms26041466.

References

Buhrman D, Price P, Rudewiczcor P . Quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry: A study of ion suppression. J Am Soc Mass Spectrom. 2013; 7(11):1099-105. DOI: 10.1016/S1044-0305(96)00072-4. View

Mashego M, Rumbold K, De Mey M, Vandamme E, Soetaert W, Heijnen J . Microbial metabolomics: past, present and future methodologies. Biotechnol Lett. 2006; 29(1):1-16. DOI: 10.1007/s10529-006-9218-0. View

Jourdan F, Breitling R, Barrett M, Gilbert D . MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics. 2007; 24(1):143-5. DOI: 10.1093/bioinformatics/btm536. View

Gieger C, Geistlinger L, Altmaier E, de Angelis M, Kronenberg F, Meitinger T . Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet. 2008; 4(11):e1000282. PMC: 2581785. DOI: 10.1371/journal.pgen.1000282. View

Kirwan J, Brennan L, Broadhurst D, Fiehn O, Cascante M, Dunn W . Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for "Precision Medicine and Pharmacometabolomics Task Group"-The Metabolomics Society Initiative). Clin Chem. 2018; 64(8):1158-1182. DOI: 10.1373/clinchem.2018.287045. View

van Gulik W . Fast sampling for quantitative microbial metabolomics. Curr Opin Biotechnol. 2010; 21(1):27-34. DOI: 10.1016/j.copbio.2010.01.008. View

Spicer R, Salek R, Steinbeck C . A decade after the metabolomics standards initiative it's time for a revision. Sci Data. 2018; 4:170138. PMC: 6038898. DOI: 10.1038/sdata.2017.138. View

Djamei A, Schipper K, Rabe F, Ghosh A, Vincon V, Kahnt J . Metabolic priming by a secreted fungal effector. Nature. 2011; 478(7369):395-8. DOI: 10.1038/nature10454. View

Guijas C, Montenegro-Burke J, Warth B, Spilker M, Siuzdak G . Metabolomics activity screening for identifying metabolites that modulate phenotype. Nat Biotechnol. 2018; 36(4):316-320. PMC: 5937131. DOI: 10.1038/nbt.4101. View

10.

Blazenovic I, Kind T, Sa M, Ji J, Vaniya A, Wancewicz B . Structure Annotation of All Mass Spectra in Untargeted Metabolomics. Anal Chem. 2019; 91(3):2155-2162. PMC: 11426395. DOI: 10.1021/acs.analchem.8b04698. View

11.

Saito K, Matsuda F . Metabolomics for functional genomics, systems biology, and biotechnology. Annu Rev Plant Biol. 2009; 61:463-89. DOI: 10.1146/annurev.arplant.043008.092035. View

12.

Wehrens R, Hageman J, van Eeuwijk F, Kooke R, Flood P, Wijnker E . Improved batch correction in untargeted MS-based metabolomics. Metabolomics. 2016; 12:88. PMC: 4796354. DOI: 10.1007/s11306-016-1015-8. View

13.

Lunn J, Feil R, Hendriks J, Gibon Y, Morcuende R, Osuna D . Sugar-induced increases in trehalose 6-phosphate are correlated with redox activation of ADPglucose pyrophosphorylase and higher rates of starch synthesis in Arabidopsis thaliana. Biochem J. 2006; 397(1):139-48. PMC: 1479759. DOI: 10.1042/BJ20060083. View

14.

Gerssen A, McElhinney M, Mulder P, Bire R, Hess P, de Boer J . Solid phase extraction for removal of matrix effects in lipophilic marine toxin analysis by liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem. 2009; 394(4):1213-26. DOI: 10.1007/s00216-009-2790-0. View

15.

Shen X, Wang R, Xiong X, Yin Y, Cai Y, Ma Z . Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics. Nat Commun. 2019; 10(1):1516. PMC: 6447530. DOI: 10.1038/s41467-019-09550-x. View

16.

Sumner L, Amberg A, Barrett D, Beale M, Beger R, Daykin C . Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics. 2013; 3(3):211-221. PMC: 3772505. DOI: 10.1007/s11306-007-0082-2. View

17.

Schiffman C, Petrick L, Perttula K, Yano Y, Carlsson H, Whitehead T . Filtering procedures for untargeted LC-MS metabolomics data. BMC Bioinformatics. 2019; 20(1):334. PMC: 6570933. DOI: 10.1186/s12859-019-2871-9. View

18.

Jarmusch A, Wang M, Aceves C, Advani R, Aguirre S, Aksenov A . ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods. 2020; 17(9):901-904. PMC: 7968862. DOI: 10.1038/s41592-020-0916-7. View

19.

Rinschen M, Ivanisevic J, Giera M, Siuzdak G . Identification of bioactive metabolites using activity metabolomics. Nat Rev Mol Cell Biol. 2019; 20(6):353-367. PMC: 6613555. DOI: 10.1038/s41580-019-0108-4. View

20.

Nakamura Y, Afendi F, Parvin A, Ono N, Tanaka K, Hirai Morita A . KNApSAcK Metabolite Activity Database for retrieving the relationships between metabolites and biological activities. Plant Cell Physiol. 2013; 55(1):e7. DOI: 10.1093/pcp/pct176. View