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A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)

Nature Protocols volume 18, pages 1017–1027 (2023)Cite this article

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Abstract

Targeted metabolite assays that measure tens or hundreds of pre-selected metabolites, typically using liquid chromatography–mass spectrometry, are increasingly being developed and applied to metabolic phenotyping studies. These are used both as standalone phenotyping methods and for the validation of putative metabolic biomarkers obtained from untargeted metabolomics studies. However, there are no widely accepted standards in the scientific community for ensuring reliability of the development and validation of targeted metabolite assays (referred to here as ‘targeted metabolomics’). Most current practices attempt to adopt, with modifications, the strict guidance provided by drug regulatory authorities for analytical methods designed largely for measuring drugs and other xenobiotic analytes. Here, the regulatory guidance provided by the European Medicines Agency, US Food and Drug Administration and International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use are summarized. In this Perspective, we have adapted these guidelines and propose a less onerous ‘tiered’ approach to evaluate the reliability of a wide range of metabolomics analyses, addressing the need for community-accepted, harmonized guidelines for tiers other than full validation. This ‘fit-for-purpose’ tiered approach comprises four levels—discovery, screening, qualification and validation—and is discussed in the context of a range of targeted and untargeted metabolomics assays. Issues arising with targeted multiplexed metabolomics assays, and how these might be addressed, are considered. Furthermore, guidance is provided to assist the community with selecting the appropriate degree of reliability for a series of well-defined applications of metabolomics.

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Fig. 1: Validation workflow steps and positioning of the suggested tiered framework.

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Acknowledgements

Funding was provided by the Medical Research Council (grant reference: MR/S010483/1) to the MAP/UK project. Wellcome Trust provided support for LIPID MAPS (203014/Z/16/Z) to V.B.O’D.

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Author notes

  1. A list of authors and their affiliations appears in the Supplementary Note.

Authors and Affiliations

  1. Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Leicester, UK

    Sarir Sarmad & Toru Suzuki

  2. Phenome Centre Birmingham, University of Birmingham, Birmingham, UK

    Mark R. Viant

  3. Centre for Metabolomics Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, UK

    Warwick B. Dunn & Royston Goodacre

  4. Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK

    Warwick B. Dunn

  5. Division of Systems Medicine, Department of Metabolism, Digestion & Reproduction, Imperial College London, London, UK

    Ian D. Wilson

  6. The National Phenome Centre, Department of Metabolism, Digestion & Reproduction, Imperial College London, London, UK

    Katie E. Chappell & Matthew R. Lewis

  7. School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK

    Julian L. Griffin

  8. Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK

    Valerie B. O’Donnell & Brendon Naicker

  9. The Institute of Medical Science, The University of Tokyo, Tokyo, Japan

    Toru Suzuki

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Consortia

UK Consortium on Metabolic Phenotyping (MAP/UK)

  • Mark R. Viant
  • , Warwick B. Dunn
  • , Royston Goodacre
  • , Valerie B. O’Donnell
  • , Matthew R. Lewis
  •  & Toru Suzuki

Contributions

The content of the present manuscript was discussed by MAP/UK consortium members and then written up by S.S. and T.S. under the latter’s supervision and guidance. Scientific input and critical review were provided by M.R.L., I.D.W., M.R.V., R.G., W.B.D, J.L.G., V.B.O’D., K.E.C. and B.N.

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Correspondence to Toru Suzuki.

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Nature Protocols thanks Jianguo Xia and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Key references using this protocol

Thompson, J. W. Anal. Chem. 91, 14407–14416 (2019): https://doi.org/10.1021/acs.analchem.9b02908

Lewis, M. et al. Preprint at ChemRxiv https://doi.org/10.26434/chemrxiv-2022-nq9k0 (2022).

Israr, M. Z. Am. Heart. J. 234, 71–80 (2021): https://doi.org/10.1016/j.ahj.2021.01.006

Supplementary information

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Supplementary Tables 1 and 2

Supplementary Note

Core members of the MAP/UK consortium

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Sarmad, S., Viant, M.R., Dunn, W.B. et al. A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK). Nat Protoc 18, 1017–1027 (2023). https://doi.org/10.1038/s41596-022-00801-8

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