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ReDU: a framework to find and reanalyze public mass spectrometry data

Nature Methods volume 17, pages 901–904 (2020)Cite this article

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Abstract

We present ReDU (https://redu.ucsd.edu/), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one’s own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.

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Fig. 1: ReDU framework and illustrative public ReDU data analyses.
Fig. 2: Repository-scale molecular networking of public data in ReDU.

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Data availability

Source data for the results presented in this paper are available on GitHub (https://github.com/mwang87/ReDU-MS2-GNPS/tree/master/examples). All curated sample information can be downloaded from the ReDU homepage (https://redu.ucsd.edu/) by selecting ‘Download Database’. The current version of the ReDU information used to generate the results in this paper is archived in the GNPS/MassIVE repository (http://gnps.ucsd.edu). The accession number is MSV000084206 (https://doi.org/10.25345/C5407D).

Code availability

All software is citable using https://doi.org/10.5281/zenodo.3924422. Up-to-date developments of ReDU are available in GitHub (https://github.com/mwang87/ReDU-MS2-GNPS), with corresponding documentation (https://github.com/mwang87/ReDU-MS2-Documentation).

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Acknowledgements

We thank the individuals involved in the funding, administration, sample collection and data acquisition of the public data used in ReDU. We recognize the financial support of the US National Institutes of Health (P41 GM103484, R03 CA211211, R01 LM013115 and R01 GM107550), the Sloan Foundation (R.K.), the Gordon and Betty Moore Foundation (P.C.D., N.B., K.L.M.), a FAPESP fellowship (2018/24865-4), the American Society for Mass Spectrometry (A.K.J.), NSF grants IOS-1656481 (P.C.D. and A.M.C.R.) and ABI-1759980, Netherlands eScience Center no. ASDI.2017.030 (J.J.J.v.d.H.), the Krupp Endowed Fund (R. Coras), the US Office of Naval Research (N00014-15-1-2809) and the University of California, San Diego, Center for Microbiome Innovation SEED grants.

Author information

Author notes

  1. These authors contributed equally: Alan K. Jarmusch, Mingxun Wang, Christine M. Aceves.

Authors and Affiliations

  1. Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA

    Alan K. Jarmusch, Mingxun Wang, Christine M. Aceves, Rohit S. Advani, Shaden Aguirre, Alexander A. Aksenov, Allegra T. Aron, Anelize Bauermeister, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Emmanuel O. Elijah, Madeleine Ernst, Julia M. Gauglitz, Emily C. Gentry, Makhai Husband, Kenneth L. Jones II, Aileen Lu, Michael J. Meehan, Alexey V. Melnik, Ngoc Hung Nguyen, Louis Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Nicole Sikora, Justin J. J. van der Hooft, Fernando Vargas, Kelly C. Weldon & Pieter C. Dorrestein

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

    Alan K. Jarmusch, Mingxun Wang, Christine M. Aceves, Rohit S. Advani, Shaden Aguirre, Alexander A. Aksenov, Allegra T. Aron, Sanjana Bolleddu, Amina Bouslimani, Andres Mauricio Caraballo Rodriguez, Rama Chaar, Emmanuel O. Elijah, Madeleine Ernst, Julia M. Gauglitz, Emily C. Gentry, Makhai Husband, Kenneth L. Jones II, Aileen Lu, Michael J. Meehan, Alexey V. Melnik, Ngoc Hung Nguyen, Louis Felix Nothias, Mélissa Nothias-Esposito, Morgan Panitchpakdi, Daniel Petras, Nicole Sikora, Fernando Vargas, Kelly C. Weldon, Nuno Bandeira & Pieter C. Dorrestein

  3. Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA

    Gajender Aleti

  4. Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil

    Anelize Bauermeister

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

    Roxana Coras

  6. Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark

    Madeleine Ernst

  7. Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK

    Scott A. Jarmusch

  8. Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic

    Zdenek Kamenik

  9. TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France

    Audrey Le Gouellec

  10. Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA

    Laura-Isobel McCall

  11. Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA

    Kerry L. McPhail

  12. Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany

    Riya C. Menezes

  13. Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia

    Yessica Alejandra Montoya Giraldo

  14. Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA

    Daniel Petras

  15. Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA

    Robert A. Quinn

  16. Bioinformatics Group, Wageningen University, Wageningen, the Netherlands

    Justin J. J. van der Hooft

  17. Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA

    Fernando Vargas

  18. Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA

    Alison Vrbanac, Rob Knight & Pieter C. Dorrestein

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

    Kelly C. Weldon, Rob Knight, Nuno Bandeira & Pieter C. Dorrestein

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

    Rob Knight & Nuno Bandeira

  21. Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA

    Rob Knight

Authors
  1. Alan K. Jarmusch
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  2. Mingxun Wang
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  3. Christine M. Aceves
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  4. Rohit S. Advani
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  38. Justin J. J. van der Hooft
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  39. Fernando Vargas
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  42. Rob Knight
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  44. Pieter C. Dorrestein
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Contributions

A.K.J., M.W. and P.C.D. developed the ReDU concept. A.K.J., M.W. and C.M.A. wrote code and engineered the ReDU infrastructure. A.K.J., C.M.A., R.S.A., S.A., A.A.A., G.A., A.T.A., A. Bauermeister, S.B., A. Bouslimani, A.M.C.R., R. Chaar, R. Coras, E.O.E., J.J.J.v.d.H., J.M.G., E.C.G., M.H., K.L.J., Z.K., A.L.G., A.L., L.-I.M., K.L.M., M.J.M., A.V.M., R.C.M., Y.A.M.G., N.H.N., L.F.N., M.E., M.N.E., M.P., D.P., R.Q., N.S., F.V., A.V. and K.C.W. curated metadata enabling ReDU. A.K.J., M.W., C.M.A., S.A.J., L.-I.M., M.E., J.J.J.v.d.H., J.M.G., M.P. and P.C.D. tested the ReDU infrastructure and provided feedback. A.K.J., M.W., C.M.A., M.E., J.J.J.v.d.H., R.K., N.B. and P.C.D. wrote and edited the manuscript. R.K., N.B. and P.C.D. provided supervision and funding support.

Corresponding author

Correspondence to Pieter C. Dorrestein.

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Competing interests

P.C.D. is a scientific advisor for Sirenas LLC, Galileio and Cybele Microbiome and scientific advisor and co-founder of Enveda. M.W. is a founder of Ometa Labs LLC. A.A. is a consultant for Ometa Labs LLC.

Additional information

Peer review information Allison Doerr was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Repository-scale molecular cartography enabled by ReDU.

ReDU samples with latitude and longitude information, n = 34,003, were grouped by latitude and longitude (n = 2068 different locations) and plotted colored by number of annotations per file (log10 scaled).

Extended Data Fig. 2 Comparison of bacterial cultures using Group Comparator in ReDU.

Bacterial cultures of 1280|Staphylococcus aureus (n = 49), 1423|Bacillus subtilis (n = 89), and 1883|Streptomyces (n = 7) were compared and chemical differences are illustrated by pyroGlu-Ile, staurosporine, and surfactin-C14.

Extended Data Fig 3 Repository-scale molecular networking of human blood (n = 711), fecal (n = 5,097), and urine (n = 307) supplemented by MolNetEnhancer.

(a) MolNetEnhancer enhanced molecular network in which components are colored based on Classyfire chemical class prediction. (b) Number of nodes per Classyfire chemical class prediction. Nodes without a match in Classyfire are not displayed.

Extended Data Fig 4 Molecular cartography of the distribution of drugs on the human body visualized using ili.

Descaladinose azithromycin, a drug metabolite of azithromycin, distribution in human (n = 17,117; normalized by the number of files per sample).

Supplementary information

Supplementary Information

Supplementary Discussion, Supplementary Table 1 and Supplementary Figs. 1–5.

Reporting Summary

Supplementary Table 2

Tabulated information for proposed clindamycin metabolites based on repository-scale molecular networking in ReDU.

Supplementary Video 1

The empirically observed UBERON-based location of drugs and drug metabolites observed in metabolomics data 28 August 2019–10 July 2020 processed through ReDU.

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Jarmusch, A.K., Wang, M., Aceves, C.M. et al. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods 17, 901–904 (2020). https://doi.org/10.1038/s41592-020-0916-7

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