Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Mingxun WangCenter for Computational Mass Spectrometry, UC San Diego, La Jolla, United StatesJeremy CarverCenter for Computational Mass Spectrometry, UC San Diego, La Jolla, United StatesVanessa V. PhelanCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesLaura M. SanchezCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesNeha GargCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesYao PengDepartment of Chemistry and Biochemistry, UC San Diego, La Jolla, United StatesDon D. NguyenDepartment of Chemistry and Biochemistry, UC San Diego, La Jolla, United StatesJeramie D. WatrousCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesClifford A. KaponoDepartment of Chemistry and Biochemistry, UC San Diego, La Jolla, United StatesTal Luzzatto‐KnaanCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesCarla PortoCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesAmina BouslimaniCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesAlexey V. MelnikCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesMichael J. MeehanCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesWei-Ting LiuDepartment of Microbiology and Immunology, Stanford University, Palo Alto, United StatesMax CrüsemannCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesPaul D. BoudreauCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesEduardo EsquenaziSirenas Marine Discovery, San Diego, United StatesMario Sandoval‐CalderónCentro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, MexicoRoland D. KerstenSalk Institute, Salk Institute, La Jolla, United StatesLaura PaceCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesRobert A. QuinnBiology Department, San Diego State University, San Diego, United StatesKatherine DuncanCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesCheng‐Chih HsuDepartment of Chemistry and Biochemistry, UC San Diego, La Jolla, United StatesDimitrios J. FlorosDepartment of Chemistry and Biochemistry, UC San Diego, La Jolla, United StatesRonnie G. GavilánCenter for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, PanamaKarin KleigreweCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesTrent R. NorthenGenome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United StatesRachel J. DuttonFAS Center for Systems Biology, Harvard, Cambridge, United StatesDelphine ParrotProduits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, FranceErin E. CarlsonChemistry, University of Minnesota, Minneapolis, United StatesBertrand AigleDynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, FranceCharlotte Frydenlund MichelsenDepartment of Systems Biology, Technical University of Denmark, Lyngby, DenmarkLars JelsbakDepartment of Systems Biology, Technical University of Denmark, Lyngby, DenmarkChristian SohlenkampCentro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, MexicoPavel A. PevznerCenter for Computational Mass Spectrometry, UC San Diego, La Jolla, United StatesAnna EdlundMicrobial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United StatesJeffrey S. McLeanDepartment of Periodontics, University of Washington, Seattle, United StatesJörn PielInstitute of Microbiology, ETH Zurich, Zurich, SwitzerlandBrian T. MurphyDepartment of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United StatesLena GerwickCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesChih‐Chuang LiawDepartment of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, TaiwanYuliang YangAgricultural Biotechnology Research Center, Academia Sinica, Taipei, TaiwanHans‐Ulrich HumpfInstitute of Food Chemistry, University of Münster, Münster, GermanyMaria MaanssonDepartment of Systems Biology, Technical University of Denmark, Lyngby, DenmarkRobert A. KeyzersSchool of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New ZealandAmy SimsGillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United StatesAndrew R. JohnsonDepartment of Chemistry, Indiana University, Bloomington, United StatesAshley M. SidebottomDepartment of Chemistry, Indiana University, Bloomington, United StatesBrian E. SedioCenter for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, PanamaAndreas KlitgaardDepartment of Systems Biology, Technical University of Denmark, Lyngby, DenmarkCharles B. LarsonCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesCristopher A. Boya P.Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, PanamaDaniel Torres‐MendozaCenter for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, PanamaDavid J. GonzalezCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesDenise Brentan SilvaCentro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, BrazilLucas Maciel Mauriz MarquesSchool of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, BrazilDaniel P. DemarqueSchool of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, BrazilEglė PociūtėSirenas Marine Discovery, San Diego, United StatesEllis C. O’NeillCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesEnora BriandCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesEric J. N. HelfrichInstitute of Microbiology, ETH Zurich, Zurich, SwitzerlandEve A. GranatoskyDepartment of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United StatesEvgenia GlukhovCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesFlorian RyffelInstitute of Microbiology, ETH Zurich, Zurich, SwitzerlandHailey HousonSirenas Marine Discovery, San Diego, United StatesHosein MohimaniCenter for Computational Mass Spectrometry, UC San Diego, La Jolla, United StatesJenan J. KharbushCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesYi ZengDepartment of Chemistry and Biochemistry, UC San Diego, La Jolla, United StatesJulia A. VorholtInstitute of Microbiology, ETH Zurich, Zurich, SwitzerlandKenji L. KuritaPBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United StatesPep CharusantiDepartment of Bioengineering, UC San Diego, La Jolla, United StatesKerry L. McPhailDepartment of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United StatesKristian Fog NielsenDepartment of Systems Biology, Technical University of Denmark, Lyngby, DenmarkLisa VuongSirenas Marine Discovery, San Diego, United StatesMaryam ElfekiDepartment of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United StatesMatthew F. TraxlerDepartment of Plant and Microbial Biology, UC Berkeley, Berkeley, United StatesNiclas EngeneDepartment of Biological Sciences, Florida International University, Miami, United StatesNobuhiro KoyamaCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesOliver B. ViningDepartment of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United StatesRalph S. BaricGillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United StatesRicardo SilvaSchool of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, BrazilSamantha J. MascuchCenter for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesSophie TomasiProduits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, FranceStefan JenkinsGenome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United StatesVenkat R. MacherlaSirenas Marine Discovery, San Diego, United StatesThomas HoffmanDepartment of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, GermanyVinayak AgarwalCenter for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United StatesPhilip G. WilliamsDepartment of Chemistry, University of Hawaii at Manoa, Honolulu, United StatesJingqui DaiDepartment of Chemistry, University of Hawaii at Manoa, Honolulu, United StatesRam P. NeupaneDepartment of Chemistry, University of Hawaii at Manoa, Honolulu, United StatesJoshua R. GurrDepartment of Chemistry, University of Hawaii at Manoa, Honolulu, United StatesAndrés Mauricio Caraballo‐RodríguezSchool of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, BrazilAnne LamsaDivision of Biological Sciences, UC San Diego, La Jolla, United StatesChen ZhangDepartment of Nanoengineering, UC San Diego, La Jolla, United StatesKathleen DorresteinCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesBrendan M. DugganCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesJehad AlmalitiCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United StatesPierre‐Marie AllardSchool of Pharmaceutical Sciences, University of Geneva, Geneva, SwitzerlandPrasad PhapaleStructural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
2016en
ABI
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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Citations and references
Cited by 40 references