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

  • Wang M Computer Science and Engineering, UC San Diego, La Jolla, United States.
  • Carver JJ Computer Science and Engineering, UC San Diego, La Jolla, United States.
  • Phelan VV Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Sanchez LM Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Garg N Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Peng Y Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States.
  • Nguyen DD Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States.
  • Watrous J Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Kapono CA Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States.
  • Luzzatto-Knaan T Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Porto C Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Bouslimani A Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Melnik AV Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Meehan MJ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Liu WT Department of Microbiology and Immunology, Stanford University, Palo Alto, United States.
  • Crüsemann M Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Boudreau PD Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Esquenazi E Sirenas Marine Discovery, San Diego, United States.
  • Sandoval-Calderón M Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico.
  • Kersten RD Salk Institute, Salk Institute, La Jolla, United States.
  • Pace LA Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Quinn RA Biology Department, San Diego State University, San Diego, United States.
  • Duncan KR Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.
  • Hsu CC Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States.
  • Floros DJ Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States.
  • Gavilan RG Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama.
  • Kleigrewe K Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Northen T Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States.
  • Dutton RJ FAS Center for Systems Biology, Harvard, Cambridge, United States.
  • Parrot D Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France.
  • Carlson EE Chemistry, University of Minnesota, Minneapolis, United States.
  • Aigle B Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France.
  • Michelsen CF Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
  • Jelsbak L Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
  • Sohlenkamp C Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico.
  • Pevzner P Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.
  • Edlund A Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.
  • McLean J Department of Periodontics, University of Washington, Seattle, United States.
  • Piel J Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
  • Murphy BT Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States.
  • Gerwick L Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Liaw CC Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.
  • Yang YL Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
  • Humpf HU Institute of Food Chemistry, University of Münster, Münster, Germany.
  • Maansson M Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
  • Keyzers RA School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
  • Sims AC Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States.
  • Johnson AR Department of Chemistry, Indiana University, Bloomington, United States.
  • Sidebottom AM Department of Chemistry, Indiana University, Bloomington, United States.
  • Sedio BE Smithsonian Tropical Research Institute, Ancón, Panama.
  • Klitgaard A Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
  • Larson CB Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • P CAB Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama.
  • Torres-Mendoza D Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama.
  • Gonzalez DJ Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Silva DB School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
  • Marques LM School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
  • Demarque DP School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
  • Pociute E Sirenas Marine Discovery, San Diego, United States.
  • O'Neill EC Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Briand E Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Helfrich EJN Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
  • Granatosky EA Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States.
  • Glukhov E Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Ryffel F Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
  • Houson H Sirenas Marine Discovery, San Diego, United States.
  • Mohimani H Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.
  • Kharbush JJ Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Zeng Y Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States.
  • Vorholt JA Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
  • Kurita KL PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States.
  • Charusanti P Department of Bioengineering, UC San Diego, La Jolla, United States.
  • McPhail KL Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States.
  • Nielsen KF Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
  • Vuong L Sirenas Marine Discovery, San Diego, United States.
  • Elfeki M Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States.
  • Traxler MF Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States.
  • Engene N Department of Biological Sciences, Florida International University, Miami, United States.
  • Koyama N Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Vining OB Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States.
  • Baric R Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States.
  • Silva RR School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
  • Mascuch SJ Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Tomasi S Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France.
  • Jenkins S Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States.
  • Macherla V Sirenas Marine Discovery, San Diego, United States.
  • Hoffman T Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.
  • Agarwal V Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Williams PG Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States.
  • Dai J Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States.
  • Neupane R Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States.
  • Gurr J Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States.
  • Rodríguez AMC School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
  • Lamsa A Division of Biological Sciences, UC San Diego, La Jolla, United States.
  • Zhang C Department of Nanoengineering, UC San Diego, La Jolla, United States.
  • Dorrestein K Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Duggan BM Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Almaliti J Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Allard PM School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
  • Phapale P Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Nothias LF Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France.
  • Alexandrov T Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Litaudon M Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France.
  • Wolfender JL School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
  • Kyle JE Biological Sciences, Pacific Northwest National Laboratory, Richland, United States.
  • Metz TO Biological Sciences, Pacific Northwest National Laboratory, Richland, United States.
  • Peryea T National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States.
  • Nguyen DT National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States.
  • VanLeer D National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States.
  • Shinn P National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States.
  • Jadhav A National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States.
  • Müller R Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.
  • Waters KM Biological Sciences, Pacific Northwest National Laboratory, Richland, United States.
  • Shi W School of Dentistry, UC Los Angeles, Los Angeles, United States.
  • Liu X Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
  • Zhang L Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
  • Knight R Department of Pediatrics, UC San Diego, La Jolla, United States.
  • Jensen PR Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
  • Palsson BO Department of Bioengineering, UC San Diego, La Jolla, United States.
  • Pogliano K Division of Biological Sciences, UC San Diego, La Jolla, United States.
  • Linington RG PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States.
  • Gutiérrez M Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama.
  • Lopes NP School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
  • Gerwick WH Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Moore BS Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Dorrestein PC Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
  • Bandeira N Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.
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  • 2016-08-10
Published in:
  • Nature biotechnology. - 2016
Biological Products
Data Curation
Database Management Systems
Databases, Chemical
Information Dissemination
Information Storage and Retrieval
Internationality
Mass Spectrometry
English 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.
Language
  • English
Open access status
bronze
Identifiers
Persistent URL
https://sonar.ch/global/documents/36154
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