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Quick-start infrastructure for untargeted metabolomics analysis in GNPS

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Fig. 1: The quick-start interface of GNPS can be used for molecular networking and multivariate analysis.

Code availability

The GNPS quick-start page can be accessed at https://gnps-quickstart.ucsd.edu/, and the GitHub repository for the code is available at https://github.com/mwang87/GNPS_quickstart/. We used the public MassIVE datasets MSV000085256 and MSV000083437 for demonstration.

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Acknowledgements

This research was supported in part by National Institutes of Health (NIH) awards U19AG063744, GM107550, 1RF1AG051550, R01AG061066, 1R01LM013115, P41GM103484 and R24GM127667, and National Science Foundation (NSF) award no. ABI 1759980. C.C. was funded by NIH fellowship F31AT010419, M.F.O. was also supported by CNPq-Brazil 245954/2012.

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Authors and Affiliations

  1. Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA

    Tiago F. Leao, Anelize Bauermeister, Emmanuel O. Elijah, Emily C. Gentry, Makhai Husband, Nuno Bandeira, Mingxun Wang & Pieter C. Dorrestein

  2. Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA

    Chase M. Clark

  3. Department of Medicine, University of California San Diego, La Jolla, CA, USA

    Michelli F. Oliveira

  4. Center for Computational Mass Spectrometry, University of California San Diego, La Jolla, CA, USA

    Nuno Bandeira & Mingxun Wang

  5. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA

    Nuno Bandeira

  6. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA

    Nuno Bandeira

  7. Departments of Pharmacology and Pediatrics, University of California San Diego, La Jolla, CA, USA

    Pieter C. Dorrestein

  8. Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA

    Pieter C. Dorrestein

Authors
  1. Tiago F. Leao
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  2. Chase M. Clark
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  3. Anelize Bauermeister
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  4. Emmanuel O. Elijah
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  5. Emily C. Gentry
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  6. Makhai Husband
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  7. Michelli F. Oliveira
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  8. Nuno Bandeira
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  9. Mingxun Wang
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  10. Pieter C. Dorrestein
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Contributions

M.W., N.B. and P.C.D. designed the project. M.W. and C.M.C. developed the code for the quick-start website. T.F.L. and A.B. tested the website and prepared the examples from public data. M.W. and A.B. prepared the online documentation. M.H., M.F.O., E.O.E. and E.C.G. collected the untargeted LC–MS/MS data published at MassIVE. T.F.L., M.W., N.B. and P.C.D. wrote the article, and all authors reviewed and edited the text and figure.

Corresponding authors

Correspondence to Nuno Bandeira, Mingxun Wang or Pieter C. Dorrestein.

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Competing interests

P.C.D. is a scientific advisor to Sirenas, Galileo and Cybele, and cofounder and scientific advisor to Ometa and Enveda with approval by the University of California San Diego. M.W. is a cofounder of Ometa Labs, LLC.

Additional information

Peer review information Nature Metabolism thanks Michael Lalk and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Leao, T.F., Clark, C.M., Bauermeister, A. et al. Quick-start infrastructure for untargeted metabolomics analysis in GNPS. Nat Metab 3, 880–882 (2021). https://doi.org/10.1038/s42255-021-00429-0

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