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Towards a Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature

Nature Metabolism volume 5, pages 351–354 (2023)Cite this article

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The metabolomics literature suffers from ambiguity in the nomenclature for individual metabolites, which introduces a disconnect between publications and leads to misinterpretations. This Comment proposes recommendations for metabolite annotations to engage the scientific community and publishers to adopt a more consistent approach to metabolite nomenclature.

The research field of metabolomics has grown rapidly over the past decades. One of the key prerequisites for the success of any developing scientific field is that the findings (in this case, annotated metabolites) are reported in an unambiguous and reproducible way. Although the Metabolomics Standards Initiative (MSI) has already established recommendations on how to report metadata about metabolite identifications1, insufficient emphasis has been given to metabolite nomenclature.

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Fig. 1: The structures of 1-methylhistidine and 3-methylhistidine.
Fig. 2: The nomenclature options of small molecules.

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Authors and Affiliations

  1. Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland

    Ville Koistinen & Kati Hanhineva

  2. Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio, Finland

    Ville Koistinen & Kati Hanhineva

  3. School of Pharmacy, University of Eastern Finland, Kuopio, Finland

    Olli Kärkkäinen

  4. International Agency for Research on Cancer, Lyon, France

    Pekka Keski-Rahkonen & Augustin Scalbert

  5. Tokyo University of Agriculture and Technology, Tokyo, Japan

    Hiroshi Tsugawa

  6. National Institute of Genetics, Mishima, Japan

    Masanori Arita

  7. RIKEN, Yokohama, Japan

    Masanori Arita

  8. University of Alberta, Edmonton, Alberta, Canada

    David Wishart

Authors
  1. Ville Koistinen
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  2. Olli Kärkkäinen
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  3. Pekka Keski-Rahkonen
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  4. Hiroshi Tsugawa
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  5. Augustin Scalbert
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  6. Masanori Arita
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  7. David Wishart
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  8. Kati Hanhineva
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Contributions

K.H., D.W., O.K., and V.K. formulated the concept. V.K. drafted the initial manuscript and figures. V.K., O.K., P.K.-R., H.T., A.S., M.A., D.W., and K.H. provided literature references and edited and approved the manuscript.

Corresponding author

Correspondence to Ville Koistinen.

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Competing interests

The authors declare the following competing interests: P.K.-R. and A.S.: where authors are identified as personnel of the International Agency for Research on Cancer/World Health Organization, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer/World Health Organization. V.K., O.K. and K.H. are affiliated with Afekta Technologies, Ltd. H.T., M.A. and D.W. declare no competing interests.

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Koistinen, V., Kärkkäinen, O., Keski-Rahkonen, P. et al. Towards a Rosetta stone for metabolomics: recommendations to overcome inconsistent metabolite nomenclature. Nat Metab 5, 351–354 (2023). https://doi.org/10.1038/s42255-023-00757-3

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  • DOI: https://doi.org/10.1038/s42255-023-00757-3

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