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

被引：3047

作者：

Wang, Mingxun ^{[1
,2
]}

Carver, Jeremy J. ^{[1
,2
]}

Phelan, Vanessa V. ^{[3
]}

Sanchez, Laura M. ^{[3
]}

Garg, Neha ^{[3
]}

Peng, Yao ^{[4
]}

Don Duy Nguyen ^{[4
]}

Watrous, Jeramie ^{[3
]}

Kapono, Clifford A. ^{[4
]}

Luzzatto-Knaan, Tal ^{[3
]}

Porto, Carla ^{[3
]}

Bouslimani, Amina ^{[3
]}

Melnik, Alexey V. ^{[3
]}

Meehan, Michael J. ^{[3
]}

Liu, Wei -Ting ^{[5
]}

Criisemann, Max ^{[6
]}

Boudreau, Paul D. ^{[6
]}

Esquenazi, Eduardo ^{[7
]}

Sandoval-Calderon, Mario ^{[8
]}

Kersten, Roland D. ^{[9
]}

Pace, Laura A. ^{[3
]}

Quinn, Robert A. ^{[10
]}

Duncan, Katherine R. ^{[6
,11
]}

Hsu, Cheng-Chih ^{[4
]}

Floros, Dimitrios J. ^{[4
]}

Gavilan, Ronnie G. ^{[12
]}

Kleigrewe, Karin ^{[6
]}

Northen, Trent ^{[13
]}

Dutton, Rachel J. ^{[14
]}

Parrot, Delphine ^{[15
]}

Carlson, Erin E. ^{[16
]}

Aigle, Bertrand ^{[17
]}

Michelsen, Charlotte F. ^{[18
]}

Jelsbak, Lars ^{[18
]}

Sohlenkamp, Christian ^{[8
]}

Pevzner, Pavel ^{[1
,2
]}

Edlund, Anna ^{[19
,20
]}

McLean, Jeffrey ^{[20
,21
]}

Piel, Jorn ^{[22
]}

Murphy, Brian T. ^{[23
]}

Gerwick, Lena ^{[6
]}

Liaw, Chih-Chuang ^{[24
]}

Yang, Yu-Liang ^{[25
]}

Humpf, Hans-Ulrich ^{[26
]}

Maansson, Maria ^{[18
]}

Keyzers, Robert A. ^{[27
,28
]}

Sims, Amy C. ^{[29
]}

Johnson, Andrew R. ^{[30
]}

Sidebottom, Ashley M. ^{[30
]}

Sedio, Brian E. ^{[12
,31
]}

机构：

[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

来源：

NATURE BIOTECHNOLOGY | 2016年 / 34卷 / 08期

基金：

巴西圣保罗研究基金会; 瑞士国家科学基金会; 中国国家自然科学基金; 美国国家科学基金会; 美国国家卫生研究院;

关键词：

GENE-CLUSTER; GENOME; DEREPLICATION; METABOLOMICS; IDENTIFICATION; REPOSITORY; DISCOVERY; RESOURCE; EXTRACTS;

D O I：

10.1038/nbt.3597

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页码：828 / 837

页数：10

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