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

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Creator
  • Wang, Mingxun
    • Other Affiliation: Computer Science and Engineering; University of California (UC) San Diego
  • Carver, Jeremy J.
    • Other Affiliation: Computer Science and Engineering; University of California (UC) San Diego
  • Phelan, Vanessa V.
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Sanchez, Laura M.
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Garg, Neha
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Peng, Yao
    • Other Affiliation: Department of Chemistry and Biochemistry; UC San Diego
  • Nguyen, Don Duy
    • Other Affiliation: Department of Chemistry and Biochemistry; UC San Diego
  • Watrous, Jeramie
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Kapono, Clifford A.
    • Other Affiliation: Department of Chemistry and Biochemistry; UC San Diego
  • Luzzatto-Knaan, Tal
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Porto, Carla
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Bouslimani, Amina
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Melnik, Alexey V.
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Meehan, Michael J.
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Liu, Wei-Ting
    • Other Affiliation: Department of Microbiology and Immunology; Stanford University
  • Crüsemann, Max
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Boudreau, Paul D.
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Esquenazi, Eduardo
    • Other Affiliation: Sirenas Marine Discovery
  • Sandoval-Calderón, Mario
    • Other Affiliation: Centro de Ciencias Genómicas; Universidad Nacional Autonoma de Mexico
  • Kersten, Roland D.
    • Other Affiliation: Salk Institute
  • Pace, Laura A.
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Quinn, Robert A.
    • Other Affiliation: Biology Department; San Diego State University
  • Duncan, Katherine R.
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Hsu, Cheng-Chih
    • Other Affiliation: Department of Chemistry and Biochemistry; UC San Diego
  • Floros, Dimitrios J.
    • Other Affiliation: Department of Chemistry and Biochemistry; UC San Diego
  • Gavilan, Ronnie G.
    • Other Affiliation: Center for Drug Discovery and Biodiversity; INDICASAT
  • Kleigrewe, Karin
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Northen, Trent
    • Other Affiliation: Genome Dynamics; Lawrence Berkeley National Laboratory
  • Dutton, Rachel J.
    • Other Affiliation: FAS Center for Systems Biology
  • Parrot, Delphine
    • Other Affiliation: Produits naturels - Synthèses - Chimie Médicinale; University of Rennes 1
  • Carlson, Erin E.
    • Other Affiliation: Department of Chemistry; University of Minnesota
  • Aigle, Bertrand
    • Other Affiliation: Dynamique des Génomes et Adaptation Microbienne; University of Lorraine
  • Michelsen, Charlotte F.
    • Other Affiliation: Department of Systems Biology; Technical University of Denmark
  • Jelsbak, Lars
    • Other Affiliation: Department of Systems Biology; Technical University of Denmark
  • Sohlenkamp, Christian
    • Other Affiliation: Centro de Ciencias Genómicas; Universidad Nacional Autonoma de Mexico
  • Pevzner, Pavel
    • Other Affiliation: Computer Science and Engineering; University of California (UC) San Diego
  • Edlund, Anna
    • Other Affiliation: Microbial and Environmental Genomics; J. Craig Venter Institute
  • McLean, Jeffrey
    • Other Affiliation: Department of Periodontics; University of Washington
  • Piel, Jörn
    • Other Affiliation: Institute of Microbiology; ETH Zurich
  • Murphy, Brian T.
    • Other Affiliation: Department of Medicinal Chemistry and Pharmacognosy; University of Illinois Chicago
  • Gerwick, Lena
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Liaw, Chih-Chuang
    • Other Affiliation: Department of Marine Biotechnology and Resources; National Sun Yat-sen University
  • Yang, Yu-Liang
    • Other Affiliation: Agricultural Biotechnology Research Center; Academia Sinica
  • Humpf, Hans-Ulrich
    • Other Affiliation: Institute of Food Chemistry; University of Münster
  • Maansson, Maria
    • Other Affiliation: Department of Systems Biology; Technical University of Denmark
  • Keyzers, Robert A.
    • Other Affiliation: School of Chemical and Physical Sciences; Centre for Biodiscovery; Victoria University of Wellington
  • Sims, Amy C.
    • Affiliation: Gillings School of Global Public Health, Department of Epidemiology
  • Johnson, Andrew R.
    • Other Affiliation: Department of Chemistry; Indiana University
  • Sidebottom, Ashley M.
    • Other Affiliation: Department of Chemistry; Indiana University
  • Sedio, Brian E.
    • Other Affiliation: Center for Drug Discovery and Biodiversity; INDICASAT
  • Klitgaard, Andreas
    • Other Affiliation: Department of Systems Biology; Technical University of Denmark
  • Larson, Charles B.
    • Other Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Boya, Cristopher A.P.
    • Other Affiliation: Center for Drug Discovery and Biodiversity; INDICASAT
  • Torres-Mendoza, Daniel
    • Other Affiliation: Center for Drug Discovery and Biodiversity; INDICASAT
  • Gonzalez, David J.
    • Other Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Silva, Denise B.
    • Other Affiliation: School of Pharmaceutical Sciences of Ribeirao Preto; University of São Paulo
  • Marques, Lucas M.
    • Other Affiliation: School of Pharmaceutical Sciences of Ribeirao Preto; University of São Paulo
  • Demarque, Daniel P.
    • Other Affiliation: School of Pharmaceutical Sciences of Ribeirao Preto; University of São Paulo
  • Pociute, Egle
    • Other Affiliation: Sirenas Marine Discovery
  • O'Neill, Ellis C.
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Briand, Enora
    • Other Affiliation: UMR CNRS 6553 ECOBIO; University of Rennes 1
  • Helfrich, Eric J. N.
    • Other Affiliation: Institute of Microbiology; ETH Zurich
  • Granatosky, Eve A.
    • Other Affiliation: Department of Chemistry and Biochemistry; University of Notre Dame
  • Glukhov, Evgenia
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Ryffel, Florian
    • Other Affiliation: Institute of Microbiology; ETH Zurich
  • Houson, Hailey
    • Other Affiliation: Sirenas Marine Discovery
  • Mohimani, Hosein
    • Other Affiliation: Center for Computational Mass Spectrometry; UC San Diego
  • Kharbush, Jenan J.
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Zeng, Yi
    • Other Affiliation: Department of Chemistry and Biochemistry; UC San Diego
  • Vorholt, Julia A.
    • Other Affiliation: Institute of Microbiology; ETH Zurich
  • Kurita, Kenji L.
    • Other Affiliation: PBSci-Chemistry and Biochemistry Department; UC Santa Cruz
  • Charusanti, Pep
    • Other Affiliation: Department of Bioengineering; UC San Diego
  • McPhail, Kerry L.
    • Other Affiliation: Department of Pharmaceutical Sciences; College of Pharmacy; Oregon State University
  • Nielsen, Kristian Fog
    • Other Affiliation: Department of Systems Biology; Technical University of Denmark
  • Vuong, Lisa
    • Other Affiliation: Sirenas Marine Discovery
  • Elfeki, Maryam
    • Other Affiliation: Department of Medicinal Chemistry and Pharmacognosy; University of Illinois Chicago
  • Traxler, Matthew F.
    • Other Affiliation: Department of Plant and Microbial Biology; UC Berkeley
  • Engene, Niclas
    • Other Affiliation: Department of Biological Sciences; Florida International University
  • Koyama, Nobuhiro
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Vining, Oliver B.
    • Other Affiliation: Department of Pharmaceutical Sciences; College of Pharmacy; Oregon State University
  • Baric, Ralph
    • Affiliation: Gillings School of Global Public Health, Department of Epidemiology
  • Silva, Ricardo R.
    • Other Affiliation: School of Pharmaceutical Sciences of Ribeirao Preto; University of São Paulo
  • Mascuch, Samantha J.
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Tomasi, Sophie
    • Other Affiliation: Produits naturels - Synthèses - Chimie Médicinale; University of Rennes 1
  • Jenkins, Stefan
    • Other Affiliation: Genome Dynamics; Lawrence Berkeley National Laboratory
  • Macherla, Venkat
    • Other Affiliation: Sirenas Marine Discovery
  • Hoffman, Thomas
    • Other Affiliation: Department of Pharmaceutical Biotechnology; Helmholtz Institute for Pharmaceutical Research Saarland
  • Agarwal, Vinayak
    • Other Affiliation: Center for Oceans and Human Health; Scripps Institute of Oceanography; UC San Diego
  • Williams, Philip G.
    • Other Affiliation: Department of Chemistry; University of Hawaii at Manoa
  • Dai, Jingqui
    • Other Affiliation: Department of Chemistry; University of Hawaii at Manoa
  • Neupane, Ram
    • Other Affiliation: Department of Chemistry; University of Hawaii at Manoa
  • Gurr, Joshua
    • Other Affiliation: Department of Chemistry; University of Hawaii at Manoa
  • Rodríguez, Andrés M. C.
    • Other Affiliation: School of Pharmaceutical Sciences of Ribeirao Preto; University of São Paulo
  • Lamsa, Anne
    • Other Affiliation: Division of Biological Sciences; UC San Diego
  • Zhang, Chen
    • Other Affiliation: Department of Nanoengineering; UC San Diego
  • Dorrestein, Kathleen
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Duggan, Brendan M.
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Almaliti, Jehad
    • Other Affiliation: Collaborative Mass Spectrometry Innovation Center; Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Allard, Pierre-Marie
    • Other Affiliation: School of Pharmaceutical Sciences; University of Geneva
  • Phapale, Prasad
    • Other Affiliation: Structural and Computational Biology; European Molecular Biology Laboratory
  • Nothias, Louis-Felix
    • Other Affiliation: Institut de Chimie des Substances Naturelles; CNRS-ICSN; UPR 2301; Labex CEBA; University of Paris-Saclay
  • Alexandrov, Theodore
    • Other Affiliation: Structural and Computational Biology; European Molecular Biology Laboratory
  • Litaudon, Marc
    • Other Affiliation: Institut de Chimie des Substances Naturelles; CNRS-ICSN; UPR 2301; Labex CEBA; University of Paris-Saclay
  • Wolfender, Jean-Luc
    • Other Affiliation: School of Pharmaceutical Sciences; University of Geneva
  • Kyle, Jennifer E.
    • Other Affiliation: Biological Sciences; Pacific Northwest National Laboratory
  • Metz, Thomas O.
    • Other Affiliation: Biological Sciences; Pacific Northwest National Laboratory
  • Peryea, Tyler
    • Other Affiliation: National Center for Advancing Translational Sciences; National Institutes of Health
  • Nguyen, Dac-Trung
    • Other Affiliation: National Center for Advancing Translational Sciences; National Institutes of Health
  • VanLeer, Danielle
    • Other Affiliation: National Center for Advancing Translational Sciences; National Institutes of Health
  • Shinn, Paul
    • Other Affiliation: National Center for Advancing Translational Sciences; National Institutes of Health
  • Jadhav, Ajit
    • Other Affiliation: National Center for Advancing Translational Sciences; National Institutes of Health
  • Müller, Rolf
    • Other Affiliation: Department of Pharmaceutical Biotechnology; Helmholtz Institute for Pharmaceutical Research Saarland
  • Waters, Katrina M.
    • Other Affiliation: Biological Sciences; Pacific Northwest National Laboratory
  • Shi, Wenyuan
    • Other Affiliation: School of Dentistry; UC Los Angeles
  • Liu, Xueting
    • Other Affiliation: Institute of Microbiology; Chinese Academy of Sciences
  • Zhang, Lixin
    • Other Affiliation: Institute of Microbiology; Chinese Academy of Sciences
  • Knight, Rob
    • Other Affiliation: Department of Pediatrics; UC San Diego
  • Jensen, Paul R.
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Palsson, Bernhard Ø
    • Other Affiliation: Department of Bioengineering; UC San Diego
  • Pogliano, Kit
    • Other Affiliation: Division of Biological Sciences; UC San Diego
  • Linington, Roger G.
    • Other Affiliation: PBSci-Chemistry and Biochemistry Department; UC Santa Cruz
  • Gutiérrez, Marcelino
    • Other Affiliation: Center for Drug Discovery and Biodiversity; INDICASAT
  • Lopes, Norberto P.
    • Other Affiliation: School of Pharmaceutical Sciences of Ribeirao Preto; University of São Paulo
  • Gerwick, William H.
    • Other Affiliation: Center for Marine Biotechnology and Biomedicine; Scripps Institute of Oceanography; UC San Diego
  • Moore, Bradley S.
    • Other Affiliation: Center for Oceans and Human Health; Scripps Institute of Oceanography; UC San Diego
  • Dorrestein, Pieter C.
    • Other Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
  • Bandeira, Nuno
    • Other Affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences; UC San Diego
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 techniques are well-suited to high-throughput characterization of natural products, 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.
Date of publication
Keyword
DOI
Identifier
Resource type
  • Article
Rights statement
  • In Copyright
Journal title
  • Nature Biotechnology
Journal volume
  • 34
Journal issue
  • 8
Page start
  • 828
Page end
  • 837
Language
  • English
ISSN
  • 1087-0156
  • 1546-1696

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