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Nat Biotechnol. 2016 Aug 9;34(8):828-837. doi: 10.1038/nbt.3597.

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

Wang M#1,2, Carver JJ#1,2, Phelan VV#3, Sanchez LM#3, Garg N#3, Peng Y#4, Nguyen DD4, Watrous J3, Kapono CA4, Luzzatto-Knaan T3, Porto C3, Bouslimani A3, Melnik AV3, Meehan MJ3, Liu WT5, Crüsemann M6, Boudreau PD6, Esquenazi E7, Sandoval-Calderón M8, Kersten RD9, Pace LA3, Quinn RA10, Duncan KR11,6, Hsu CC4, Floros DJ4, Gavilan RG12, Kleigrewe K6, Northen T13, Dutton RJ14, Parrot D15, Carlson EE16, Aigle B17, Michelsen CF18, Jelsbak L18, Sohlenkamp C8, Pevzner P2,1, Edlund A19,20, McLean J21,20, Piel J22, Murphy BT23, Gerwick L6, Liaw CC24, Yang YL25, Humpf HU26, Maansson M18, Keyzers RA27, Sims AC28, Johnson AR29, Sidebottom AM29, Sedio BE30,12, Klitgaard A18, Larson CB6,31, P CAB12, Torres-Mendoza D12, Gonzalez DJ31,3, Silva DB32,33, Marques LM32, Demarque DP32, Pociute E7, O'Neill EC6, Briand E6,34, Helfrich EJN22, Granatosky EA35, Glukhov E6, Ryffel F22, Houson H7, Mohimani H2, Kharbush JJ6, Zeng Y4, Vorholt JA22, Kurita KL36, Charusanti P37, McPhail KL38, Nielsen KF18, Vuong L7, Elfeki M23, Traxler MF39, Engene N40, Koyama N3, Vining OB38, Baric R28, Silva RR32, Mascuch SJ6, Tomasi S15, Jenkins S13, Macherla V7, Hoffman T41, Agarwal V42, Williams PG43, Dai J43, Neupane R43, Gurr J43, Rodríguez AMC32, Lamsa A44, Zhang C45, Dorrestein K3, Duggan BM3, Almaliti J3, Allard PM46, Phapale P47, Nothias LF48, Alexandrov T47, Litaudon M48, Wolfender JL46, Kyle JE49, Metz TO49, Peryea T50, Nguyen DT50, VanLeer D50, Shinn P50, Jadhav A50, Müller R41, Waters KM49, Shi W20, Liu X51, Zhang L51, Knight R52, Jensen PR6, Palsson BO37, Pogliano K44, Linington RG36, Gutiérrez M12, Lopes NP32, Gerwick WH3,6, Moore BS3,6,42, Dorrestein PC3,6,31, Bandeira N2,3,31.

Author information

1
Computer Science and Engineering, UC San Diego, La Jolla, United States.
2
Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.
3
Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
4
Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States.
5
Department of Microbiology and Immunology, Stanford University, Palo Alto, United States.
6
Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
7
Sirenas Marine Discovery, San Diego, United States.
8
Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico.
9
Salk Institute, Salk Institute, La Jolla, United States.
10
Biology Department, San Diego State University, San Diego, United States.
11
Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.
12
Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama.
13
Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States.
14
FAS Center for Systems Biology, Harvard, Cambridge, United States.
15
Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France.
16
Chemistry, University of Minnesota, Minneapolis, United States.
17
Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France.
18
Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
19
Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.
20
School of Dentistry, UC Los Angeles, Los Angeles, United States.
21
Department of Periodontics, University of Washington, Seattle, United States.
22
Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
23
Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States.
24
Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.
25
Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
26
Institute of Food Chemistry, University of Münster, Münster, Germany.
27
School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
28
Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States.
29
Department of Chemistry, Indiana University, Bloomington, United States.
30
Smithsonian Tropical Research Institute, Ancón, Panama.
31
Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.
32
School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.
33
Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil.
34
UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France.
35
Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States.
36
PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States.
37
Department of Bioengineering, UC San Diego, La Jolla, United States.
38
Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States.
39
Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States.
40
Department of Biological Sciences, Florida International University, Miami, United States.
41
Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.
42
Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.
43
Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States.
44
Division of Biological Sciences, UC San Diego, La Jolla, United States.
45
Department of Nanoengineering, UC San Diego, La Jolla, United States.
46
School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
47
Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.
48
Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France.
49
Biological Sciences, Pacific Northwest National Laboratory, Richland, United States.
50
National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States.
51
Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
52
Department of Pediatrics, UC San Diego, La Jolla, United States.
#
Contributed equally

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.

PMID:
27504778
PMCID:
PMC5321674
DOI:
10.1038/nbt.3597
[Indexed for MEDLINE]
Free PMC Article

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