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

Type Article
Date 2016-08
Language English
Author(s) Wang Mingxun1, 2, Carver Jeremy J.1, 2, Phelan Vanessa V.3, Sanchez Laura M.3, Garg Neha3, Peng Yao4, Don Duy Nguyen 4, Watrous Jeramie3, Kapono Clifford A.4, Luzzatto-Knaan Tal3, Porto CarlaORCID3, Bouslimani Amina3, Melnik Alexey V.3, Meehan Michael J.3, Liu Wei -Ting5, Criisemann Max6, Boudreau Paul D.6, Esquenazi Eduardo7, Sandoval-Calderon MarioORCID8, Kersten Roland D.9, Pace Laura A.3, Quinn Robert A.10, Duncan Katherine R.ORCID6, 11, Hsu Cheng-Chih4, Floros Dimitrios J.4, Gavilan Ronnie G.12, Kleigrewe Karin6, Northen TrentORCID13, Dutton Rachel J.14, Parrot Delphine15, Carlson Erin E.16, Aigle Bertrand17, Michelsen Charlotte F.18, Jelsbak Lars18, Sohlenkamp Christian8, Pevzner Pavel1, 2, Edlund Anna19, 20, McLean Jeffrey20, 21, Piel Jorn22, Murphy Brian T.23, Gerwick Lena6, Liaw Chih-Chuang24, Yang Yu-Liang25, Humpf Hans-Ulrich26, Maansson Maria18, Keyzers Robert A.27, 28, Sims Amy C.29, Johnson Andrew R.30, Sidebottom Ashley M.30, Sedio Brian E.12, 31, Klitgaard AndreasORCID18, Larson Charles B.6, 32, Boya p Cristopher A.12, Torres-Mendoza DanielORCID12, Gonzalez David J.3, 32, Silva Denise B.33, 34, Marques Lucas M.33, Demarque Daniel P.33, Pociute Egle7, O'Neill Ellis C.6, Briand EnoraORCID6, 35, Helfrich Eric J. N.22, Granatosky Eve A.36, Glukhov Evgenia6, Ryffel Florian22, Houson Hailey7, Mohimani Hosein2, Kharbush Jenan J.6, Zeng Yi4, Vorholt Julia A.22, Kurita Kenji L.37, Charusanti PepORCID38, McPhail Kerry L.39, Nielsen Kristian Fog18, Vuong Lisa7, Elfeki Maryam23, Traxler Matthew F.40, Engene Niclas41, Koyama Nobuhiro3, Vining Oliver B.39, Baric Ralph29, Silva Ricardo R.33, Mascuch Samantha J.6, Tomasi Sophie15, Jenkins Stefan13, Macherla Venkat7, Hoffman Thomas42, Agarwal Vinayak43, Williams Philip G.44, Dai Jingqui44, Neupane Ram44, Gurr Joshua44, Rodriguez Andres M. C.33, Lamsa Anne45, Zhang Chen46, Dorrestein Kathleen3, Duggan Brendan M.3, Almaliti Jehad3, Allard Pierre-Marie47, Phapale Prasad48, Nothias Louis-Felix49, Alexandrovr Theodore48, Litaudon Marc49, Wolfender Jean-Luc47, Kyle Jennifer E.50, Metz Thomas O.50, Peryea Tyler51, Dac-Trung Nguyen 51, Vanleer Danielle51, Shinn Paul51, Jadhav Ajit51, Muller RolfORCID42, Waters Katrina M.50, Shi Wenyuan20, Liu Xueting52, Zhang Lixin, Knight RobORCID53, Jensen Paul R.6, Palsson Bernhard O.38, Pogliano KitORCID45, Linington Roger G.37, Gutierrez Marcelino12, Lopes Norberto P.33, Gerwick William H.3, 6, Moore Bradley S.3, 6, 43, Dorrestein Pieter C.3, 6, 32, Bandeira Nuno2, 3, 32
Affiliation(s) 1 : Univ Calif San Diego, Comp Sci & Engn, La Jolla, CA 92093 USA.
2 : Univ Calif San Diego, Ctr Computat Mass Spectrometry, La Jolla, CA USA.
3 : Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, Collaborat Mass Spectrometry Innovat Ctr, La Jolla, CA USA.
4 : Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA USA.
5 : Stanford Univ, Dept Microbiol & Immunol, Palo Alto, CA 94304 USA.
6 : Univ Calif San Diego, Scripps Inst Oceanog, Ctr Marine Biotechnol & Biomed, La Jolla, CA USA.
7 : Sirenas Marine Discovery, San Diego, CA USA.
8 : Univ Nacl Autonoma Mexico, Ctr Ciencias Genom, Cuernavaca, Morelos, Mexico.
9 : Salk Inst Biol Studies, La Jolla, CA USA.
10 : San Diego State Univ, Dept Biol, San Diego, CA 92182 USA.
11 : Scottish Marine Inst, Scottish Assoc Marine Sci, Oban, Argyll, Scotland.
12 : INDICASAT, Ctr Drug Discovery & Biodivers, City Of Knowledge, Panama.
13 : Lawrence Berkeley Natl Lab, Genome Dynam, Berkeley, CA USA.
14 : Harvard, FAS Ctr Syst Biol, Cambridge, MA USA.
15 : Univ Rennes 1, Prod Nat Synth Chim Med, Rennes, France.
16 : Univ Minnesota, Dept Chem, 207 Pleasant St SE, Minneapolis, MN 55455 USA.
17 : Univ Lorraine, Dynam Genomes & Adaptat Microbienne, Vandoeuvre Les Nancy, France.
18 : Tech Univ Denmark, Dept Syst Biol, Lyngby, Denmark.
19 : J Craig Venter Inst, Microbial & Environm Genom, La Jolla, CA USA.
20 : UC Los Angeles, Sch Dent, Los Angeles, CA USA.
21 : Univ Washington, Dept Periodont, Seattle, WA 98195 USA.
22 : Swiss Fed Inst Technol, Inst Microbiol, Zurich, Switzerland.
23 : Univ Illinois, Dept Med Chem & Pharmacognosy, Chicago, IL USA.
24 : Natl Sun Yat Sen Univ, Dept Marine Biotechnol & Resources, Kaohsiung, Taiwan.
25 : Acad Sinica, Agr Biotechnol Res Ctr, Taipei, Taiwan.
26 : Univ Munster, Inst Food Chem, Munster, Germany.
27 : Victoria Univ Wellington, Sch Chem & Phys Sci, Wellington, New Zealand.
28 : Victoria Univ Wellington, Ctr Biodiscovery, Wellington, New Zealand.
29 : Univ North Carolina Chapel Hill, Dept Epidemiol, Gillings Sch Global Publ Hlth, Chapel Hill, NC USA.
30 : Indiana Univ, Dept Chem, Bloomington, IN USA.
31 : Smithsonian Trop Res Inst, Ancon, Panama.
32 : Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA USA.
33 : Univ Sao Paulo, Sch Pharmaceut Sci Ribeirao Preto, Sao Paulo, Brazil.
34 : Univ Fed Mato Grosso do Sul, Ctr Ciencias Biol & Saude, Campo Grande, Brazil.
35 : Univ Rennes 1, CNRS, UMR 6553, ECOBIO, Rennes, France.
36 : Univ Notre Dame, Dept Chem & Biochem, Notre Dame, IN 46556 USA.
37 : UC Santa Cruz, PBSci Chem & Biochem Dept, Santa Cruz, CA USA.
38 : Univ Calif San Diego, Dept Bioengn, La Jolla, CA USA.
39 : Oregon State Univ, Coll Pharm, Dept Pharmaceut Sci, Corvallis, OR 97331 USA.
40 : Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA USA.
41 : Florida Int Univ, Dept Biol Sci, Miami, FL 33199 USA.
42 : Helmholtz Inst Pharmaceut Res Saarland, Dept Pharmaceut Biotechnol, Saarbrucken, Germany.
43 : Univ Calif San Diego, Scripps Inst Oceanog, Ctr Oceans & Human Hlth, La Jolla, CA USA.
44 : Univ Hawaii Manoa, Dept Chem, Honolulu, HI 96822 USA.
45 : Univ Calif San Diego, Div Biol Sci, La Jolla, CA USA.
46 : Univ Calif San Diego, Dept Nanoengn, La Jolla, CA USA.
47 : Univ Geneva, Sch Pharmaceut Sci, Geneva, Switzerland.
48 : European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
49 : Univ Paris Saclay, Labex CEBA, ICSN, CNRS,UPR 2301, Gif Sur Yvette, France.
50 : Pacific NW Natl Lab, Biol Sci, Richland, WA 99352 USA.
51 : NIH, Natl Ctr Adv Translat Sci, Rockville, MD USA.
52 : Chinese Acad Sci, Inst Microbiol, Beijing, Peoples R China.
53 : Univ Calif San Diego, Dept Pediat, La Jolla, CA USA.
Source Nature Biotechnology (1087-0156) (Nature Publishing Group), 2016-08 , Vol. 34 , N. 8 , P. 828-837
DOI 10.1038/nbt.3597
WOS© Times Cited 2375
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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Supplementary Tables 1–4 and 6–14, Supplementary Figures 1–20, Supplementary Notes 1–12 and Supplementary Methods 51 6 MB Open access
Supplementary Table 5 148 KB Open access
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Wang Mingxun, Carver Jeremy J., Phelan Vanessa V., Sanchez Laura M., Garg Neha, Peng Yao, Don Duy Nguyen, Watrous Jeramie, Kapono Clifford A., Luzzatto-Knaan Tal, Porto Carla, Bouslimani Amina, Melnik Alexey V., Meehan Michael J., Liu Wei -Ting, Criisemann Max, Boudreau Paul D., Esquenazi Eduardo, Sandoval-Calderon Mario, Kersten Roland D., Pace Laura A., Quinn Robert A., Duncan Katherine R., Hsu Cheng-Chih, Floros Dimitrios J., Gavilan Ronnie G., Kleigrewe Karin, Northen Trent, Dutton Rachel J., Parrot Delphine, Carlson Erin E., Aigle Bertrand, Michelsen Charlotte F., Jelsbak Lars, Sohlenkamp Christian, Pevzner Pavel, Edlund Anna, McLean Jeffrey, Piel Jorn, Murphy Brian T., Gerwick Lena, Liaw Chih-Chuang, Yang Yu-Liang, Humpf Hans-Ulrich, Maansson Maria, Keyzers Robert A., Sims Amy C., Johnson Andrew R., Sidebottom Ashley M., Sedio Brian E., Klitgaard Andreas, Larson Charles B., Boya p Cristopher A., Torres-Mendoza Daniel, Gonzalez David J., Silva Denise B., Marques Lucas M., Demarque Daniel P., Pociute Egle, O'Neill Ellis C., Briand Enora, Helfrich Eric J. N., Granatosky Eve A., Glukhov Evgenia, Ryffel Florian, Houson Hailey, Mohimani Hosein, Kharbush Jenan J., Zeng Yi, Vorholt Julia A., Kurita Kenji L., Charusanti Pep, McPhail Kerry L., Nielsen Kristian Fog, Vuong Lisa, Elfeki Maryam, Traxler Matthew F., Engene Niclas, Koyama Nobuhiro, Vining Oliver B., Baric Ralph, Silva Ricardo R., Mascuch Samantha J., Tomasi Sophie, Jenkins Stefan, Macherla Venkat, Hoffman Thomas, Agarwal Vinayak, Williams Philip G., Dai Jingqui, Neupane Ram, Gurr Joshua, Rodriguez Andres M. C., Lamsa Anne, Zhang Chen, Dorrestein Kathleen, Duggan Brendan M., Almaliti Jehad, Allard Pierre-Marie, Phapale Prasad, Nothias Louis-Felix, Alexandrovr Theodore, Litaudon Marc, Wolfender Jean-Luc, Kyle Jennifer E., Metz Thomas O., Peryea Tyler, Dac-Trung Nguyen, Vanleer Danielle, Shinn Paul, Jadhav Ajit, Muller Rolf, Waters Katrina M., Shi Wenyuan, Liu Xueting, Zhang Lixin, Knight Rob, Jensen Paul R., Palsson Bernhard O., Pogliano Kit, Linington Roger G., Gutierrez Marcelino, Lopes Norberto P., Gerwick William H., Moore Bradley S., Dorrestein Pieter C., Bandeira Nuno (2016). Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology, 34(8), 828-837. Publisher's official version : https://doi.org/10.1038/nbt.3597 , Open Access version : https://archimer.ifremer.fr/doc/00408/51939/