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Spatial metabolomics: from a niche field towards a driver of innovation

Nature Metabolism volume 5, pages 1443–1445 (2023)Cite this article

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Spatial metabolomics has matured and is driving innovation in mass spectrometry, metabolomics and spatial omics. With exciting discoveries, complementary capabilities and increasing accessibility, it has secured its place in the spatial biology toolbox, showing promise in biology, medicine and pharmacology.

Spatial metabolomics, the field of science and technology concerned with detecting and interpreting metabolites in situ within their spatial context, has undergone a substantial transformation in recent years1,2. Early adopters are equipped with all the essential tools for spatial interrogation of metabolism: robust and accessible protocols for sample preparation, fast and high-resolution instruments, and user-friendly software for data analysis and interpretation3. Recent reports have demonstrated the capabilities of spatial metabolomics in detecting metabolic states of cells and their heterogeneity4,5, probing host–microbe metabolic interactions at the micrometre scale6, revealing metabolic cell fate trajectories7 and creating spatial maps of metabolic activity8. Concurrently, there is an increasing interest in metabolomics in biology, where there is a growing appreciation of the roles of metabolites in fuelling and regulating molecular and cellular processes9, and of the importance of non-genetic metabolic factors in sustaining tissue homeostasis. This is complemented by interest in metabolism in clinical applications — for example, in cancer, to modulate the functions of cells in the tumour microenvironment10, and in metabolic and immune diseases and cancer immunotherapy by targeting the metabolism of immune cells11. These advances and trends have brought spatial metabolomics, into the spotlight. In this Comment, we review both the state of the art and the potential of spatial metabolomics, highlight how it drives innovation in metabolomics and mass spectrometry, and discuss its potential for addressing outstanding questions in spatial biology by complementing other spatial omics techniques.

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Acknowledgements

I thank B. Wadie from our team at EMBL for feedback on the manuscript draft; M. Becker, who was my first guide into imaging MS; P. Dorrestein and J. Watrious, who introduced me to metabolomics; and to our team members at EMBL with whom I had the pleasure of learning other spatial omics and multi-omics.

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Authors and Affiliations

  1. Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

    Theodore Alexandrov

  2. Metabolomics Core Facility, EMBL, Heidelberg, Germany

    Theodore Alexandrov

  3. Molecular Medicine Partnership Unit, EMBL and Heidelberg University, Heidelberg, Germany

    Theodore Alexandrov

  4. Bio Studio, BioInnovation Institute, Copenhagen, Denmark

    Theodore Alexandrov

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  1. Theodore Alexandrov
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Correspondence to Theodore Alexandrov.

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Competing interests

T.A. holds several patents in spatial metabolomics and is a BioStudio Faculty member at the BioInnovation Institute in Copenhagen, where he leads commercialization of the spatial single-cell metabolomics technology.

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Nature Metabolism thanks Ton Rabelink for his contribution to the peer review of this work.

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Alexandrov, T. Spatial metabolomics: from a niche field towards a driver of innovation. Nat Metab 5, 1443–1445 (2023). https://doi.org/10.1038/s42255-023-00881-0

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