Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Comment
  • Published:

Quick tips for re-using metabolomics data

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

References

  1. Fernie, A. R., Trethewey, R. N., Krotzky, A. J. & Willmitzer, L. Nat. Rev. Mol. Cell. Biol. 5, 763–769 (2004).

    Article  CAS  PubMed  Google Scholar 

  2. Sud, M. et al. Nucleic Acids Res. 44, D463–D470 (2016).

    Article  CAS  PubMed  Google Scholar 

  3. Haug, K. et al. Nucleic Acids Res. 48, D440–D444 (2020).

    CAS  PubMed  Google Scholar 

  4. Lokhov, P. G., Maslov, D. L., Kharibin, O. N., Balashova, E. E. & Archakov, A. I. BioData Mining 10, 10 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Cajka, T. & Fiehn, O. Anal. Chem. 88, 524–545 (2016).

    Article  CAS  PubMed  Google Scholar 

  6. Bennett, B. D., Yuan, J., Kimball, E. H. & Rabinowitz, J. D. Nat. Protoc. 3, 1299–1311 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Hasselblad, V. & Hedges, L. V. Psychological Bulletin 117, 167–178 (1995).

    Article  CAS  PubMed  Google Scholar 

  8. Patti, G. J., Tautenhahn, R. & Siuzdak, G. Nat. Protoc. 7, 508–516 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Guasch-Ferré, M. et al. Diabetes Care 39, 833–846 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Broadhurst, D. et al. Metabolomics 14, 72 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Chaleckis, R., Meister, I., Zhang, P. & Wheelock, C. E. Curr. Opin. Biotechnol. 55, 44–50 (2019).

    Article  CAS  PubMed  Google Scholar 

  12. Sindelar, M. & Patti, G. J. J. Am. Chem. Soc. 142, 9097–9105 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Sumner, L. W. et al. Metabolomics 3, 211–221 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Mahieu, N. G. & Patti, G. J. Anal. Chem. 89, 10397–10406 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Fahy, E. & Subramaniam, S. Nat. Methods 17, 1173–1174 (2020).

    Article  CAS  PubMed  Google Scholar 

  16. Stanstrup, J. et al. Metabolites 9, 200 (2019).

    Article  CAS  PubMed Central  Google Scholar 

  17. Spicer, R., Salek, R. M., Moreno, P., Cañueto, D. & Steinbeck, C. Metabolomics 13, 106 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Tautenhahn, R., Patti, G. J., Rinehart, D. & Siuzdak, G. Anal. Chem. 84, 5035–5039 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Pang, Z. et al. Nucleic Acids Res. 49, W388–W396 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Petras, D. et al. Nat. Methods 19, 134–136 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Smirnov, A., Liao, Y., Fahy, E., Subramaniam, S. & Du, X. Anal. Chem. 93, 12213–12220 (2021).

    Article  CAS  PubMed  Google Scholar 

  22. Myers, O. D., Sumner, S. J., Li, S., Barnes, S. & Du, X. Anal. Chem. 89, 8689–8695 (2017).

    Article  CAS  PubMed  Google Scholar 

  23. Alseekh, S. et al. Nat. Methods 18, 747–756 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Chang, H.-Y. et al. Anal. Chem. 93, 1912–1923 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Gary J. Patti.

Ethics declarations

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.

Peer review

Peer review information

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

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41556-022-01019-2

Search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research