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GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser

Nature Methods volume 19, pages 134–136 (2022)Cite this article

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To the Editor — The importance of providing open and transparent solutions to use, share, inspect and reproduce mass spectrometry (MS) data analysis is becoming more apparent. To address these challenges, we developed a collaborative interactive web application, the GNPS Dashboard (https://gnps-lcms.ucsd.edu), to enable remote and synchronous collaborative research in a common analysis environment for MS data analysis (similar to collaborative text editing in browser-based word processors, such as Google Docs).

The disruptions to office and laboratory workspaces resulting from the COVID-19 pandemic, including campus closures, telework and stay-at-home orders, increased the need for online collaborative approaches to perform scientific research. Most solutions for the analysis of MS data are geared for exploration on a local workstation that lacks synchronous collaborative data exploration, requiring specific software packages, knowledge of data storage locations, familiarity with file transfer protocols and often conversion of data into compatible formats1,2,3,4. Commercial data exploration solutions usually lack universality and are costly, creating additional hurdles to data accessibility, preventing collaborators, reviewers and readers of scientific publications from inspecting MS data to verify interpretations. However, commercial software offers deep access to proprietary vendor-specific data formats and unique data analysis capabilities, for example, creation of private databases. More broadly, as scientific data are becoming more complex, scientific reproducibility is a challenge. Therefore, there is a growing mandate by both funding bodies and journals to make mass spectrometry data (and other data) adherent to FAIR (findable, accessible, interoperable and reusable).

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Fig. 1: Overview of the GNPS Dashboard in the data analysis ecosystem.

Code availability

While the GNPS Dashboard is accessible as a free public web service, it is possible to locally install the GNPS Dashboard to function with local data sources, making collaborative analysis and sharing possible privately within an institution when necessary. The source code is available through the GNPS web environment and GitHub, enabling quick installation on local servers. The GNPS Dashboard source code can be found on GitHub: https://github.com/mwang87/GNPS_LCMSDashboard under a modified UCSD BSD License. The GNPS Dataset Explorer source code can be found on GitHub: https://github.com/mwang87/GNPS_DatasetExplorer under an MIT License. Further implementation details can be found in Supplementary Methods.

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Acknowledgements

This work was, in part, supported by the National Institutes of Health (NIH) with grant numbers U19AG063744, U2CDK119886, OT2 OD030544, GM107550, R03CA211211, R24GM127667, 1R01LM013115 and P41GM103484, the National Science Foundation (NSF) with grants IOS-1656475 and ABI 1759980, and the Gordon and Betty Moore Foundation with grant GBMF7622. D.P. was supported by the Deutsche Forschungsgemeinschaft through the CMFI Cluster of Excellence (EXC 2124). V.V.P. was supported by NIH grant R35GM128690. N.B. and B.P. were supported by NIH grant P41-GM103484. M.T.M. was supported by NSF grant CHE-1845230. D.B. was supported by NSF grant DUE 16-25354. The I.M laboratory was supported by grants from the European Research Council (grant number 640384) and from the Israel Science Foundation (ISF number 1947/19). T.R.N., B.B. and K.L. were supported by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, which is supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. A.W.P. and D.A.C.J. were supported by NIH grant R00 GM 118762. This research was supported in part by the Intramural Research Program of the National Institute of Environmental Health Sciences of the NIH (ES103363-01). Furthermore, we would like to thank T. de Rond, L.-I. McCall, W. Bittremieux, K. Weldon and E. Gentry for testing the software and suggesting updates. We would like to thank V. Sharma, for working on the standalone MSView app during her Masters degree research 12 years ago, which provided some visualization inspiration for the GNPS Dashboard. We thank C. O’Donovan and the team at MetaboLights for developing a well-documented API. Lastly, we thank all members of the research community who make their data publicly accessible, which contributes to open, transparent and reproducible science.

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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

    Daniel Petras, Allegra T. Aron, Alan K. Jarmusch, Morgan Panitchpakdi, Robin Schmid, Pieter C. Dorrestein & Mingxun Wang

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

    Daniel Petras, Andrew E. Allen, Monica Thukral & Pieter C. Dorrestein

  3. CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Medicine, University of Tübingen, Tübingen, Germany

    Daniel Petras

  4. Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA

    Vanessa V. Phelan

  5. Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA

    Deepa Acharya & Jo Handelsman

  6. Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA

    Andrew E. Allen & Monica Thukral

  7. Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA

    Nuno Bandeira & Benjamin Pullman

  8. DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Benjamin P. Bowen, Katherine Louie & Trent R. Northen

  9. Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA

    Deirdre Belle-Oudry & Michael T. Marty

  10. Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany

    Simon Boecker

  11. Department of Chemistry, University of Utah, Salt Lake City, UT, USA

    Dale A. Cummings Jr. & Aaron W. Puri

  12. Henry Eyring Center for Cell & Genome Science, University of Utah, Salt Lake City, UT, USA

    Dale A. Cummings Jr. & Aaron W. Puri

  13. School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA

    Jessica M. Deutsch & Neha Garg

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

    Eoin Fahy & Shankar Subramaniam

  15. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Rachel Gregor

  16. BIoactivity for Sustainable Development Group (BIODESS), Department of Chemistry, University of Costa Rica, San Jose, Costa Rica

    Mirtha Navarro-Hoyos

  17. Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA

    Alan K. Jarmusch

  18. Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark

    Scott A. Jarmusch

  19. Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA

    Katherine N. Maloney

  20. Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva, Israel

    Michael M. Meijler

  21. National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel

    Michael M. Meijler & Itzhak Mizrahi

  22. Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel

    Itzhak Mizrahi

  23. Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA

    Rachel L. Neve

  24. Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain

    Carlos Molina-Santiago

  25. Centro Nacional de Innovaciones Biotecnologicas (CENIBiot), CeNAT-CONARE, 1174-1200, San Jose, Costa Rica

    Felipe Vasquez-Castro

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

    Pieter C. Dorrestein

  27. Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA

    Pieter C. Dorrestein & Mingxun Wang

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  1. Daniel Petras
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  2. Vanessa V. Phelan
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  35. Mingxun Wang
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Contributions

M.W. and D.P. conceived the project. M.W. developed the software for GNPS Dashboard and GNPS Dataset Explorer. M.W., D.P., V.V.P. and P.C.D. provided guidance and supervision. M.W., D.P., V.V.P., K.N.M., A.T.A., A.K.J., B.P., D.A.C.J., A.W.P., C.M.S., M.T., N.G., N.B. and P.C.D. tested and offered user feedback for the GNPS Dashboard. S.S. and E.F. implemented the APIs in Metabolomics Workbench to support GNPS Dashboard. T.N., B.B. and K.L. facilitated making metabolomics data in Genome Portal available in GNPS Dashboard. M.W., D.P., V.V.P., K.N.M., A.T.A., A.K.J., S.A.J., D.A., B.P., D.A.C.J., A.W.P., C.M.S., M.T., A.E.A., R.S., N.B., S.B., M.T.M., D.B.O., M.N.H., R.G., M.M.M., I.M., J.H., F.V.C., J.M.D., N.G., N.B., R.L.N. and P.C.D. wrote use cases for the GNPS Dashboard Supplemental Information. P.C.D. provided funding for the project. P.C.D., M.W., V.V.P. and D.P. wrote the draft manuscript. All authors edited and approved the final manuscript.

Corresponding author

Correspondence to Mingxun Wang.

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Competing interests

P.C.D. is a scientific advisor of Sirenas, Galileo and Cybele, and scientific advisor and co-founder of Ometa Labs LLC and Enveda with approval by the UC San Diego. M.W. is a founder of Ometa Labs LLC. T.R.N. is an advisor of Brightseed Bio.

Additional information

Peer review information Nature Methods thanks Juan Antonio Vizcaino, Jean-Luc Wolfender and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Supplementary Information

Supplementary Information

Supplemental Notes 1 and 2, Supplementary Methods, Data Availability, Supplementary Fig. 1.

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Petras, D., Phelan, V.V., Acharya, D. et al. GNPS Dashboard: collaborative exploration of mass spectrometry data in the web browser. Nat Methods 19, 134–136 (2022). https://doi.org/10.1038/s41592-021-01339-5

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