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

Nature Biotechnology · 2016 · Vol. 34(8) · pp. 828–837

Mingxun Wang✉(UC San Diego Health System)Jeremy Carver(UC San Diego Health System)Vanessa V. Phelan(University of California San Diego)Laura M. Sanchez(University of California San Diego)Neha Garg(University of California San Diego)Yao Peng(UC San Diego Health System)Don D. Nguyen(UC San Diego Health System)Jeramie D. Watrous(University of California San Diego)Clifford A. Kapono(UC San Diego Health System)Tal Luzzatto‐Knaan(University of California San Diego)Carla Porto(University of California San Diego)Amina Bouslimani(University of California San Diego)Alexey V. Melnik(University of California San Diego)Michael J. Meehan(University of California San Diego)Wei-Ting Liu(Palo Alto University)Max Crüsemann(Scripps Institution of Oceanography)Paul D. Boudreau(Scripps Institution of Oceanography)Eduardo Esquenazi(Sirenas (United States))Mario Sandoval‐Calderón(Universidad Nacional Autónoma de México)Roland D. Kersten(Salk Institute for Biological Studies)Laura Pace(University of California San Diego)Robert A. Quinn(San Diego State University)Katherine Duncan(Scripps Institution of Oceanography)Cheng‐Chih Hsu(UC San Diego Health System)Dimitrios J. Floros(UC San Diego Health System)Ronnie G. Gavilán(Instituto de Investigaciones Científicas y Servicios de Alta Tecnología)Karin Kleigrewe(Scripps Institution of Oceanography)Trent R. Northen(Lawrence Berkeley National Laboratory)Rachel J. Dutton(Center for Systems Biology)Delphine Parrot(École Nationale Supérieure de Chimie de Rennes)Erin E. Carlson(University of Minnesota)Bertrand Aigle(Dynamique des Génomes et Adaptation Microbienne)Charlotte Frydenlund Michelsen(Technical University of Denmark)Lars Jelsbak(Technical University of Denmark)Christian Sohlenkamp(Universidad Nacional Autónoma de México)Pavel A. Pevzner(UC San Diego Health System)Anna Edlund(J. Craig Venter Institute)Jeffrey S. McLean(University of Washington)Jörn Piel(ETH Zurich)Brian T. Murphy(University of Illinois Chicago)Lena Gerwick(Scripps Institution of Oceanography)Chih‐Chuang Liaw(National Sun Yat-sen University)Yuliang Yang(Agricultural Biotechnology Research Center, Academia Sinica)Hans‐Ulrich Humpf(University of Münster)Maria Maansson(Technical University of Denmark)Robert A. Keyzers(Victoria University of Wellington)Amy Sims(University of North Carolina at Chapel Hill)Andrew R. Johnson(Indiana University Bloomington)Ashley M. Sidebottom(Indiana University Bloomington)Brian E. Sedio(Smithsonian Tropical Research Institute)Andreas Klitgaard(Technical University of Denmark)Charles B. Larson(Scripps Institution of Oceanography)Cristopher A. Boya P.(Instituto de Investigaciones Científicas y Servicios de Alta Tecnología)Daniel Torres‐Mendoza(Instituto de Investigaciones Científicas y Servicios de Alta Tecnología)David J. Gonzalez(University of California San Diego)Denise Brentan Silva(Universidade Federal de Mato Grosso do Sul)Lucas Maciel Mauriz Marques(Universidade de São Paulo)Daniel P. Demarque(Universidade de São Paulo)Eglė Pociūtė(Sirenas (United States))Ellis C. O’Neill(Scripps Institution of Oceanography)Enora Briand(Centre National de la Recherche Scientifique)Eric J. N. Helfrich(ETH Zurich)Eve A. Granatosky(University of Notre Dame)Evgenia Glukhov(Scripps Institution of Oceanography)Florian Ryffel(ETH Zurich)Hailey Houson(Sirenas (United States))Hosein Mohimani(UC San Diego Health System)Jenan J. Kharbush(Scripps Institution of Oceanography)Yi Zeng(UC San Diego Health System)Julia A. Vorholt(ETH Zurich)Kenji L. Kurita(University of California, Santa Cruz)Pep Charusanti(University of California San Diego)Kerry L. McPhail(Oregon State University)Kristian Fog Nielsen(Technical University of Denmark)Lisa Vuong(Sirenas (United States))Maryam Elfeki(University of Illinois Chicago)Matthew F. Traxler(Berkeley College)Niclas Engene(Florida International University)Nobuhiro Koyama(University of California San Diego)Oliver B. Vining(Oregon State University)Ralph S. Baric(University of North Carolina at Chapel Hill)Ricardo Silva(Universidade de São Paulo)Samantha J. Mascuch(Scripps Institution of Oceanography)Sophie Tomasi(École Nationale Supérieure de Chimie de Rennes)Stefan Jenkins(Lawrence Berkeley National Laboratory)Venkat R. Macherla(Sirenas (United States))Thomas Hoffman(Helmholtz Institute for Pharmaceutical Research Saarland)Vinayak Agarwal(Scripps Institution of Oceanography)Philip G. Williams(University of Hawaiʻi at Mānoa)Jingqui Dai(University of Hawaiʻi at Mānoa)Ram P. Neupane(University of Hawaiʻi at Mānoa)Joshua R. Gurr(University of Hawaiʻi at Mānoa)Andrés Mauricio Caraballo‐Rodríguez(Universidade de São Paulo)Anne Lamsa(UC San Diego Health System)Chen Zhang(University of California San Diego)Kathleen Dorrestein(University of California San Diego)Brendan M. Duggan(University of California San Diego)Jehad Almaliti(University of California San Diego)Pierre‐Marie Allard(University of Geneva)Prasad Phapale(European Molecular Biology Laboratory)Louis‐Félix Nothias(Centre National de la Recherche Scientifique)Theodore Alexandrov(European Molecular Biology Laboratory)Marc Litaudon(Centre National de la Recherche Scientifique)Jean‐Luc Wolfender(University of Geneva)Jennifer Kyle(Pacific Northwest National Laboratory)Thomas Metz(Pacific Northwest National Laboratory)Tyler Peryea(National Institutes of Health)Ðắc-Trung Nguyễn(National Institutes of Health)Danielle VanLeer(National Institutes of Health)Paul Shinn(National Institutes of Health)Ajit Jadhav(National Institutes of Health)Rolf Müller(Helmholtz Institute for Pharmaceutical Research Saarland)Katrina M. Waters(Pacific Northwest National Laboratory)Wenyuan Shi(UtopiaCompression (United States))Xueting Liu(Chinese Academy of Sciences)Lixin Zhang(Chinese Academy of Sciences)Rob Knight(UC San Diego Health System)Paul R. Jensen(Scripps Institution of Oceanography)Bernhard Ø. Palsson(University of California San Diego)Kit Pogliano(UC San Diego Health System)Roger G. Linington(University of California, Santa Cruz)Marcelino Gutiérrez(Instituto de Investigaciones Científicas y Servicios de Alta Tecnología)Norberto Peporine Lopes(Universidade de São Paulo)William H. Gerwick(Scripps Institution of Oceanography)Bradley S. Moore(Scripps Institution of Oceanography)Pieter C. Dorrestein(Scripps Institution of Oceanography)Nuno Bandeira(UC San Diego Health System)

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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.

Metabolomics and Mass Spectrometry Studies Species Distribution and Climate Change Microbial Community Ecology and PhysiologyData curationNatural (archaeology)Mass spectrometryBusinessData sharingComputational biologyChemistryData scienceWorld Wide WebComputer science

MeSH terms

Biological ProductsDatabase Management SystemsMass SpectrometryInformation Storage and RetrievalInformation DisseminationInternationalityDatabases, ChemicalData Curation

Funding

National Science Foundation
U.S. Department of Defense
Smithsonian Institution
U.S. Department of Health and Human Services
Research Corporation for Science Advancement
University of California Institute for Mexico and the United States
United States - Israel Binational Agricultural Research and Development Fund
Villum Fonden
Indian National Science Academy
Deutscher Akademischer Austauschdienst
Deutsche Forschungsgemeinschaft
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Fundação de Amparo à Pesquisa do Estado de São Paulo
National Natural Science Foundation of China
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Consejo Nacional de Ciencia y Tecnología
Conselho Nacional de Desenvolvimento Científico e Tecnológico
Novo Nordisk
Ministry of Science and Technology, Taiwan
Danmarks Frie Forskningsfond
Augustinus Fonden
Novo Nordisk Fonden
Key Laboratory of Micro-Systems and Micro-Structures Manufacturing, Ministry of Education, Harbin Institute of Technology
National Institutes of Health
Oregon Sea Grant, Oregon State University
Ciência sem Fronteiras
National Institute of Allergy and Infectious Diseases
FP7 People: Marie-Curie Actions