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Quick tips for re-using metabolomics data

Nature Cell Biology volume 24, pages 1560–1562 (2022)Cite this article

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Publicly shared metabolomics data may contain key answers to central questions in cell biology, but re-use of the data is complicated by the lack of standardized experimental and computational methods in the field. This Comment provides some tips to help ensure that shared metabolomics data are re-used appropriately.

Metabolomics is a well-established profiling science that is widely recognized as an integral component of systems biology1. With the exponential rise in the number of metabolomics experiments performed over the past two decades, data-sharing repositories have become crucial to extending the impact of the field. Owing to resources such as the Metabolomics Workbench2 and MetaboLights3, investigators around the world now have access to thousands of metabolomics data files. The challenge for data re-use, however, is the diversity in experimental design, methodology and organization of the shared data. These differences complicate the ways in which shared data can be interpreted and re-used to explore additional questions beyond the scope of the original studies. To help facilitate this process and promote the appropriate re-use of shared data, here we provide tips that might be valuable for researchers who wish to take advantage of public resources in the field but do not have expertise in metabolomics. Although the list is not exhaustive, we aimed to include issues commonly discussed among our collaborators. A detailed discussion of each point is beyond the scope of this Comment, but we direct readers to several excellent reviews in the sections that follow.

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Acknowledgements

We are indebted to M. Schwaiger-Haber and M. Sindelar for their feedback and suggestions on manuscript content. We thank the NIH (awards R35ES028365 and R01GM134081) for their financial support.

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Authors and Affiliations

  1. Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA

    Ethan Stancliffe & Gary J. Patti

  2. Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA

    Ethan Stancliffe & Gary J. Patti

  3. Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA

    Ethan Stancliffe & Gary J. Patti

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  1. Ethan Stancliffe
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Correspondence to Gary J. Patti.

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Competing interests

G.J.P. is a scientific advisory board member for Cambridge Isotope Laboratories. The Patti laboratory has a collaborative agreement with Thermo Fisher Scientific and Agilent Technologies.

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Nature Cell Biology thanks Alisdair Fernie and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Stancliffe, E., Patti, G.J. Quick tips for re-using metabolomics data. Nat Cell Biol 24, 1560–1562 (2022). https://doi.org/10.1038/s41556-022-01019-2

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