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Review
. 2025 May 26;23(1):5.
doi: 10.1186/s12953-025-00241-8.

Mass-spectrometry based metabolomics: an overview of workflows, strategies, data analysis and applications

Kosar Hajnajafi  1 , Mohammad Askandar Iqbal  2   3
Affiliations
Review

Mass-spectrometry based metabolomics: an overview of workflows, strategies, data analysis and applications

Kosar Hajnajafi et al. Proteome Sci. .

Abstract

Background: Metabolomics, a burgeoning field within systems biology, focuses on the comprehensive study of small molecules present in biological systems. Mass spectrometry (MS) has emerged as a powerful tool for metabolomic analysis due to its high sensitivity, resolution, and ability to characterize a wide range of metabolites thus offering deep insights into the metabolic profiles of living systems.

Aim of review: This review provides an overview of the methodologies, workflows, strategies, data analysis techniques, and applications associated with mass spectrometry-based metabolomics.

Key scientific concepts of review: We discuss workflows, key strategies, experimental procedures, data analysis techniques, and diverse applications of metabolomics in various research domains. Nuances of sample preparation, metabolite extraction, separation using chromatographic techniques, mass spectrometry analysis, and data processing are elaborated. Moreover, standards, quality controls, metabolite annotation, software for statistical and pathway analysis are also covered. In conclusion, this review aims to facilitate the understanding and adoption of mass spectrometry-based metabolomics by newcomers and researchers alike by providing a foundational understanding and insights into the current state and future directions of this dynamic field.

Keywords: Analytes; LC–MS; Mass spectrometry; Metabolic fingerprinting; Metabolites; Metabolomics.

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Conflict of interest statement

Declarations. Ethics approval ad consent to participate: Not Applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Four major omics fields, from genomics, transcriptomics, proteomics and metabolomics. Metabolites like S-adenosyl methionine (SAM) and acetyl-CoA play important regulatory roles in epigenetic modifications (e.g. methylation, acetylation, respectively). TPP (Thiamine Pyrophosphate) is involved in riboswitch activation. Metabolites like SAM, lactate and acetyl-CoA are involved in post-translational modifications of proteins (e.g. methylation, lactylation and acetylation)
Fig. 2
Fig. 2
Steps involved in a typical metabolomics workflow
Fig. 3
Fig. 3
Setup and principle of a typical LC–MS instrument
See this image and copyright information in PMC

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