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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Nature Biotechnology volume 34, pages 828837 (2016) | Download Citation

Abstract

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

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Acknowledgements

This work was partially supported by US National Institutes of Health (NIH) grants 5P41GM103484-07, GM094802, AI095125, GM097509, S10RR029121, UL1RR031980, GM085770, U01TW0007401, and U01AI12316-01; N.B. was also partially supported as an Alfred P. Sloan Fellow. In addition, this work was supported by the National Institute of Allergy and Infectious Diseases (NIAID), NIH, and the Department of Health and Human Services, under Contract Number HHSN272200800060C. V.V.P. is supported by the NIH grant K01 GM103809. L.M.S. is supported by NIH IRACDA K12 GM068524 award. T.L.-K. is supported by the United States–Israel Binational Agricultural Research and Development Fund Vaadia-BARD No. FI-494-13. C.P. is supported by Science without Borders Program from CNPq. A.M.C.R. is supported by São Paulo Research Foundation (FAPESP) grant#2014/01651-8, 2012/18031-7. K.K. was supported by a fellowship within the Postdoc-Programme of the German Academic Exchange Service (DAAD). M.C. was supported by a Deutsche Forschungsgemeinschaft (D.F.G.) postdoctoral fellowship. E.B. is supported by a Marie Curie IOF Fellowship within the 7th European Community Framework Program (FP7-PEOPLE-2011-IOF, grant number 301244-CYANOMIC). C.-C.L. was supported by a grant from the Ministry of Science and Technology of Taiwan (MOST103-2628-B-110-001-MY3). P.C. and B.Ø.P. were supported by the Novo Nordisk Foundation. Lixin Zhang and Xueting Liu are supported by the National Program on Key Basic Research Project (2013BC734000) and the National Natural Science Foundation of China (81102369 and 31125002). D.P. is supported by an INSA grant, Rennes. R.R.S. is supported by FAPESP grant#2014/01884-2. D.P.D. is supported by FAPESP grant#2014/18052-0. L.M.M. is supported by FAPESP grant#2013/16496-5. D.B.S. is supported by FAPESP grant#2012/18031-7. N.P.L. is supported by FAPESP (2014/50265-3), CAPES/PNPD, CNPq-PQ 480 306385/2011-2, and CNPq-INCT_if. E.A.G. is supported by the Notre Dame Chemistry-Biochemistry-Biology Interface (CBBI) program and NIH T32 GM075762. W.S. and J.S.M. are supported by grants from the National Institutes of Health 1R01DE023810-01 and 1R01GM095373. A.E. is supported by a grant from the NIH K99DE024543. C.F.M. and L.J. are supported by the Villum Foundation VKR023113, the Augustinus Foundation 13-4656, and the Aase & Ejnar Danielsens Foundation 10-001120. M.S.-C. was supported by UC MEXUS-CONACYT Collaborative Grant CN-12-552. M.F.T. was supported by NIH grant 1F32GM089044. Contributions by B.E.S. were supported by NSF grant DEB 1010816 and a Smithsonian Institution Grand Challenges Award. E.J.N.H. and J.P. are supported by the DFG (Forschergruppe 854) and by SNF grant IZLSZ3_149025. K.F.N. and A.K. are supported by the Danish Council for Independent Research, Technology, and Production Sciences (09-064967) and the Agilent Thought Leader Program. A.C.S. and R.S.B. were supported by NIH/NIAID U19-AI106772. B.T.M. and M.E. were supported under Department of Defense grant #W81XWH-13-1-0171. Contributions by O.B.V. and K.L.M. were supported by Oregon Sea Grant NA10OAR4170059/R/BT-48, NIH 5R21AI085540, and U01TW006634-06. E.E.C., A.M.S., and A.R.J. were supported by an NSF CAREER Award, a Pew Biomedical Scholar Award (E.E.C.), a Sloan Research Fellow Award (E.E.C.), the Research Corporation for Science Advancement (Cottrell Scholar Award; E.E.C.) and an Indiana University Quantitative Chemical Biology trainee fellowship (A.R.J.). M.M. was supported by the Danish Research Council for Technology and Production Science with Sapere Aude (116262). P.-M.A. was supported by FNS for fellowship on Subside (200020_146200). We thank V. Paul, R. Taylor, L. Aluwihare, F. Rohwer, B. Pullman, J. Fang, M. Overgaard, M. Katze, R.D. Smith, S.K. Mazmanian, W. Fenical, E. Macagno, X. He, and C. Neubauer for feedback and support for their laboratory personnel to contribute to the work. We thank B. Gust and co-workers at the University of Tuebingen for assisting us to obtain Streptomyces sp. DSM5940.

Author information

Author notes

    • Mingxun Wang
    • , Jeremy J Carver
    • , Vanessa V Phelan
    • , Laura M Sanchez
    • , Neha Garg
    •  & Yao Peng

    These authors contributed equally to this work.

Affiliations

  1. Computer Science and Engineering, University of California (UC) San Diego, La Jolla, California, USA.

    • Mingxun Wang
    • , Jeremy J Carver
    •  & Pavel Pevzner
  2. Center for Computational Mass Spectrometry, UC San Diego, La Jolla, California, USA.

    • Mingxun Wang
    • , Jeremy J Carver
    • , Pavel Pevzner
    • , Hosein Mohimani
    •  & Nuno Bandeira
  3. Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA.

    • Vanessa V Phelan
    • , Laura M Sanchez
    • , Neha Garg
    • , Jeramie Watrous
    • , Tal Luzzatto-Knaan
    • , Carla Porto
    • , Amina Bouslimani
    • , Alexey V Melnik
    • , Michael J Meehan
    • , Laura A Pace
    • , David J Gonzalez
    • , Nobuhiro Koyama
    • , Kathleen Dorrestein
    • , Brendan M Duggan
    • , Jehad Almaliti
    • , William H Gerwick
    • , Bradley S Moore
    • , Pieter C Dorrestein
    •  & Nuno Bandeira
  4. Department of Chemistry and Biochemistry, UC San Diego, La Jolla, California, USA.

    • Yao Peng
    • , Don Duy Nguyen
    • , Clifford A Kapono
    • , Cheng-Chih Hsu
    • , Dimitrios J Floros
    •  & Yi Zeng
  5. Department of Microbiology and Immunology, Stanford University, Palo Alto, California, USA.

    • Wei-Ting Liu
  6. Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, California, USA.

    • Max Crüsemann
    • , Paul D Boudreau
    • , Katherine R Duncan
    • , Karin Kleigrewe
    • , Lena Gerwick
    • , Charles B Larson
    • , Ellis C O'Neill
    • , Enora Briand
    • , Evgenia Glukhov
    • , Jenan J Kharbush
    • , Samantha J Mascuch
    • , Paul R Jensen
    • , William H Gerwick
    • , Bradley S Moore
    •  & Pieter C Dorrestein
  7. Sirenas Marine Discovery, San Diego, California, USA.

    • Eduardo Esquenazi
    • , Egle Pociute
    • , Hailey Houson
    • , Lisa Vuong
    •  & Venkat Macherla
  8. Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico.

    • Mario Sandoval-Calderón
    •  & Christian Sohlenkamp
  9. Salk Institute, Salk Institute, La Jolla, California, USA.

    • Roland D Kersten
  10. Biology Department, San Diego State University, San Diego, California, USA.

    • Robert A Quinn
  11. Scottish Association for Marine Science, Scottish Marine Institute, Oban, UK.

    • Katherine R Duncan
  12. Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama.

    • Ronnie G Gavilan
    • , Brian E Sedio
    • , Cristopher A Boya P
    • , Daniel Torres-Mendoza
    •  & Marcelino Gutiérrez
  13. Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

    • Trent Northen
    •  & Stefan Jenkins
  14. FAS Center for Systems Biology, Harvard, Cambridge, Massachusetts, USA.

    • Rachel J Dutton
  15. Produits naturels – Synthèses – Chimie Médicinale, University of Rennes 1, Rennes Cedex, France.

    • Delphine Parrot
    •  & Sophie Tomasi
  16. Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA.

    • Erin E Carlson
  17. Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France.

    • Bertrand Aigle
  18. Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.

    • Charlotte F Michelsen
    • , Lars Jelsbak
    • , Maria Maansson
    • , Andreas Klitgaard
    •  & Kristian Fog Nielsen
  19. Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USA.

    • Anna Edlund
  20. School of Dentistry, UC Los Angeles, Los Angeles, California, USA.

    • Anna Edlund
    • , Jeffrey McLean
    •  & Wenyuan Shi
  21. Department of Periodontics, University of Washington, Seattle, Washington, USA.

    • Jeffrey McLean
  22. Institute of Microbiology, ETH Zurich, Zurich, Switzerland.

    • Jörn Piel
    • , Eric J N Helfrich
    • , Florian Ryffel
    •  & Julia A Vorholt
  23. Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, Illinois, USA.

    • Brian T Murphy
    •  & Maryam Elfeki
  24. Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.

    • Chih-Chuang Liaw
  25. Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.

    • Yu-Liang Yang
  26. Institute of Food Chemistry, University of Münster, Münster, Germany.

    • Hans-Ulrich Humpf
  27. School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.

    • Robert A Keyzers
  28. Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA.

    • Amy C Sims
    •  & Ralph Baric
  29. Department of Chemistry, Indiana University, Bloomington, Indiana, USA.

    • Andrew R Johnson
    •  & Ashley M Sidebottom
  30. Smithsonian Tropical Research Institute, Ancón, Panama.

    • Brian E Sedio
  31. Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA.

    • Charles B Larson
    • , David J Gonzalez
    • , Pieter C Dorrestein
    •  & Nuno Bandeira
  32. School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.

    • Denise B Silva
    • , Lucas M Marques
    • , Daniel P Demarque
    • , Ricardo R Silva
    • , Andrés M C Rodríguez
    •  & Norberto P Lopes
  33. Centro de Ciencias Biologicas e da Saude, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil.

    • Denise B Silva
  34. UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France.

    • Enora Briand
  35. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.

    • Eve A Granatosky
  36. PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, California, USA.

    • Kenji L Kurita
    •  & Roger G Linington
  37. Department of Bioengineering, UC San Diego, La Jolla, California, USA.

    • Pep Charusanti
    •  & Bernhard Ø Palsson
  38. Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA.

    • Kerry L McPhail
    •  & Oliver B Vining
  39. Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA.

    • Matthew F Traxler
  40. Department of Biological Sciences, Florida International University, Miami, Florida, USA.

    • Niclas Engene
  41. Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.

    • Thomas Hoffman
    •  & Rolf Müller
  42. Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, California, USA.

    • Vinayak Agarwal
    •  & Bradley S Moore
  43. Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii, USA.

    • Philip G Williams
    • , Jingqui Dai
    • , Ram Neupane
    •  & Joshua Gurr
  44. Division of Biological Sciences, UC San Diego, La Jolla, California, USA.

    • Anne Lamsa
    •  & Kit Pogliano
  45. Department of Nanoengineering, UC San Diego, La Jolla, California, USA.

    • Chen Zhang
  46. School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.

    • Pierre-Marie Allard
    •  & Jean-Luc Wolfender
  47. Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.

    • Prasad Phapale
    •  & Theodore Alexandrov
  48. Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France.

    • Louis-Felix Nothias
    •  & Marc Litaudon
  49. Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, USA.

    • Jennifer E Kyle
    • , Thomas O Metz
    •  & Katrina M Waters
  50. National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA.

    • Tyler Peryea
    • , Dac-Trung Nguyen
    • , Danielle VanLeer
    • , Paul Shinn
    •  & Ajit Jadhav
  51. Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

    • Xueting Liu
    •  & Lixin Zhang
  52. Department of Pediatrics, UC San Diego, La Jolla, California, USA.

    • Rob Knight

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  97. Search for Brendan M Duggan in:

  98. Search for Jehad Almaliti in:

  99. Search for Pierre-Marie Allard in:

  100. Search for Prasad Phapale in:

  101. Search for Louis-Felix Nothias in:

  102. Search for Theodore Alexandrov in:

  103. Search for Marc Litaudon in:

  104. Search for Jean-Luc Wolfender in:

  105. Search for Jennifer E Kyle in:

  106. Search for Thomas O Metz in:

  107. Search for Tyler Peryea in:

  108. Search for Dac-Trung Nguyen in:

  109. Search for Danielle VanLeer in:

  110. Search for Paul Shinn in:

  111. Search for Ajit Jadhav in:

  112. Search for Rolf Müller in:

  113. Search for Katrina M Waters in:

  114. Search for Wenyuan Shi in:

  115. Search for Xueting Liu in:

  116. Search for Lixin Zhang in:

  117. Search for Rob Knight in:

  118. Search for Paul R Jensen in:

  119. Search for Bernhard Ø Palsson in:

  120. Search for Kit Pogliano in:

  121. Search for Roger G Linington in:

  122. Search for Marcelino Gutiérrez in:

  123. Search for Norberto P Lopes in:

  124. Search for William H Gerwick in:

  125. Search for Bradley S Moore in:

  126. Search for Pieter C Dorrestein in:

  127. Search for Nuno Bandeira in:

Contributions

Design and oversight of the project: P.C.D. and N.B. Algorithms: M.W. and N.B. Website: M.W., J.J.C. In-house library acquisition and analysis: V.V.P., L.M.S., N.G., A.J., D.-T.N., D.V., E.E., E.P., H.H., P.S., T.P., V.M. User-curated library acquisition and analysis: A.C.S., A.E., J.M., W.S., W.-T.L., M.J.M., V.V.P., L.M.S., N.G., R.A.Q., A.B., C.P., T.L.-K., A.M.C.R., A.M., M.C., K.R.D., K.K., E.C.O'N., B.S.M., E.B., E.G., D.D.N., S.J.M., P.D.B., X.L., L.Z., H.-U.H., C.F.M., L.J., D.P., S.T., E.A.G., M.S.-C., C.S., K.L.K., P.-M.A., R.G.L., R.S.B., P.R.J., M.F.T., S.J., B.E.S., L.M.M., DP.D., D.B.S., N.P.L., J.P., E.J.N.H., A.K., R.A.K., J.E.K., T.O.M., P.G.W., J.D., R.N., J.G., B.A., O.B.V., K.L.M., E.E.C., A.M.S., A.R.J., R.D.K., J.J.K., K.M.W., C.-C.H., M.M., C.-C.L., Y.-L.Y., A.V.M., C.B.L., D.J.G., F.R., H.M., J.-L.W., J.M., J.A., J.W., J.A.V., K.D., K.F.N., M.L., N.E., N.K., P. Pevzner, P. Phapale, R.J.D., R.B., R.M., R.G.G., T.A., T.H., T.N., V.A., W.H.G., Y.Z. Sample preparation, data generation, and website beta testing: A.E., W.T.L., M.J.M., V.V.P., L.M.S., N.G., R.A.Q., A.B., C.P., T.L.-K., A.M.C.R., A.M., D.J.F., M.C., J.J.C., N.B., P.C.D., E.C.O., E.B., E.G., D.D.N., S.J.M., P.D.B., X.L., L.Z., C.Z., C.F.M., R.R.S., E.A.G., M.S.-C., C.S., D.P., S.T., P.-M.A., R.G.L., B.E.S., L.M.M., J.P., E.J.N.H., D.T.-M., C.A.B.P., M.E., B.T.M., O.B.V., K.L.M., E.E.C., A.M.S., A.R.J., K.R.D. GNPS documentation: M.W., V.V.P., L.M.S., C.A.K., D.D.N., R.R.S., L.A.P. Genome sequencing, assembly and targeted amplification: Y.P., P.C., R.G.G., M.G., B.Ø.P., L.G. Stenothricin GNPS data analysis: W.-T.L., V.V.P., L.M.S., Y.P., P.C.D. NMR acquisition and analysis: B.M.D., P.D.B., L.M.S. Marfey's analysis: Y.P., P.D.B. Microbiology: Y.P., A.C.S., R.S.B. Peptidogenomics analysis: Y.P., R.D.K., P.C.D. Fluorescence Microscopy: Y.P., A.L., K.P. Writing of the paper: M.W., V.V.P., L.M.S., N.G., R.K., P.C.D., and N.B.

Competing interests

N.B. has an equity interest in Digital Proteomics, LLC, a company that may potentially benefit from the research results; Digital Proteomics, LLC, was not involved in any aspects of this research. The terms of this arrangement have been reviewed and approved by the University of California, San Diego, in accordance with its conflict-of-interest policies. E.E., E.P., H.H., L.V., and V.M. are employees of Sirenas MD. P.C.D. is on the advisory board for Sirenas MD. T.A. is the Scientific Director of SCiLS GmbH.

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https://doi.org/10.1038/nbt.3597

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