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

Nature Biotechnology

Volumn 34, Issue 8, 2016, Pages 828-837

  Wang, Mingxun ^a   Carver, Jeremy J ^a   Phelan, Vanessa V ^b   Sanchez, Laura M ^b   Garg, Neha ^b   Peng, Yao ^a   Nguyen, Don Duy ^a   Watrous, Jeramie ^b   Kapono, Clifford A ^a   Luzzatto Knaan, Tal ^b   Porto, Carla ^b   Bouslimani, Amina ^b   Melnik, Alexey V ^b   Meehan, Michael J ^b   Liu, Wei Ting ^c   Crüsemann, Max ^d   Boudreau, Paul D ^d   Esquenazi, Eduardo ^e   Sandoval Calderón, Mario ^f   Kersten, Roland D ^g   Pace, Laura A ^b   Quinn, Robert A ^h   Duncan, Katherine R ^d,i   Hsu, Cheng Chih ^a   Floros, Dimitrios J ^a   Gavilan, Ronnie G ^j   Kleigrewe, Karin ^d   Northen, Trent ^k   Dutton, Rachel J ^l   Parrot, Delphine ^m   Carlson, Erin E ⁿ   Aigle, Bertrand ^o   Michelsen, Charlotte F ^p   Jelsbak, Lars ^p   Sohlenkamp, Christian ^f   Pevzner, Pavel ^a   Edlund, Anna ^q,r   McLean, Jeffrey ^r,s   Piel, Jörn ^t   Murphy, Brian T ^u   Gerwick, Lena ^d   Liaw, Chih Chuang ^v   Yang, Yu Liang ^w   Humpf, Hans Ulrich ^x   Maansson, Maria ^p   Keyzers, Robert A ^y   Sims, Amy C ^z   Johnson, Andrew R ^aa   Sidebottom, Ashley M ^aa   Sedio, Brian E ^j,ab   Klitgaard, Andreas ^p   Larson, Charles B ^b,d   Boya, Cristopher A P ^j   Torres Mendoza, Daniel ^j   Gonzalez, David J ^b   Silva, Denise B ^ac,ad   Marques, Lucas M ^ac   Demarque, Daniel P ^ac   Pociute, Egle ^e   O'Neill, Ellis C ^d   Briand, Enora ^d,ae   Helfrich, Eric J N ^t   Granatosky, Eve A ^af   Glukhov, Evgenia ^d   Ryffel, Florian ^t   Houson, Hailey ^e   Mohimani, Hosein ^a   Kharbush, Jenan J ^d   Zeng, Yi ^a   Vorholt, Julia A ^t   Kurita, Kenji L ^ag   Charusanti, Pep ^ah   McPhail, Kerry L ^ai   Nielsen, Kristian Fog ^p   Vuong, Lisa ^e   Elfeki, Maryam ^u   Traxler, Matthew F ^aj   Engene, Niclas ^ak   Koyama, Nobuhiro ^b   Vining, Oliver B ^ai   Baric, Ralph ^z   Silva, Ricardo R ^ac   Mascuch, Samantha J ^d   Tomasi, Sophie ^m   Jenkins, Stefan ^k   Macherla, Venkat ^e   Hoffman, Thomas ^al   Agarwal, Vinayak ^am   Williams, Philip G ^an   Dai, Jingqui ^an   Neupane, Ram ^an   Gurr, Joshua ^an   Rodríguez, Andrés M C ^ac   Lamsa, Anne ^ao   Zhang, Chen ^ap   Dorrestein, Kathleen ^b   Duggan, Brendan M ^b   Almaliti, Jehad ^b   Allard, Pierre Marie ^aq   Phapale, Prasad ^ar   Nothias, Louis Felix ^as   Alexandrov, Theodore ^ar   Litaudon, Marc ^as   Wolfender, Jean Luc ^aq   Kyle, Jennifer E ^at   Metz, Thomas O ^at   Peryea, Tyler ^au   Nguyen, Dac Trung ^au   VanLeer, Danielle ^au   Shinn, Paul ^au   Jadhav, Ajit ^au   Müller, Rolf ^al   Waters, Katrina M ^at   Shi, Wenyuan ^r   Liu, Xueting ^av   Zhang, Lixin ^av   Knight, Rob ^aw   Jensen, Paul R ^d   Palsson, Bernhard Ø ^ah   Pogliano, Kit ^ao   Linington, Roger G ^ag   Gutiérrez, Marcelino ^j   Lopes, Norberto P ^ac   Gerwick, William H ^b,d   Moore, Bradley S ^b,d,am   Dorrestein, Pieter C ^b,d   Bandeira, Nuno ^a,b   more..

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c STANFORD UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^e Sirenas Marine Discovery   (United States)

^f INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^g SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^h SAN DIEGO STATE UNIVERSITY   (United States)

ⁱ SCOTTISH MARINE INSTITUTE   (United Kingdom)

^j INSTITUTO DE INVESTIGACIONES CIENTÍFICAS Y SERVICIOS DE ALTA TECNOLOGÍA   (Panama)

^k LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^l HARVARD UNIVERSITY   (United States)

^m UNIVERSITÉ DE RENNES 1   (France)

ⁿ University of Minnesota   (United States)

^o UNIVERSITÉ DE LORRAINE   (France)

^p TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^q J CRAIG VENTER INSTITUTE   (United States)

^r UNIVERSITY OF CALIFORNIA   (United States)

^s UNIVERSITY OF WASHINGTON   (United States)

^t ETH ZURICH   (Switzerland)

^u UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^v NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

^w AGRICULTURAL BIOTECHNOLOGY RESEARCH CENTER   (Taiwan)

^x UNIVERSITY OF MÜNSTER   (Germany)

^y VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

^z IL   (United States)

^aa INDIANA UNIVERSITY   (United States)

^ab SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

^ac UNIVERSITY OF SÃO PAULO   (Brazil)

^ad FEDERAL UNIVERSITY OF MATO GROSSO DO SUL   (Brazil)

^ae UNIVERSITÉ DE RENNES 1   (France)

^af UNIVERSITY OF NOTRE DAME   (United States)

^ag UNIVERSITY OF CALIFORNIA   (United States)

^ah UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^ai OREGON STATE UNIVERSITY   (United States)

^aj UNIVERSITY OF CALIFORNIA   (United States)

^ak FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^al SAARLAND UNIVERSITY   (Germany)

^am UNIVERSITY OF CALIFORNIA   (United States)

^an UNIVERSITY OF HAWAII   (United States)

^ao UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^ap UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^aq UNIVERSITY OF GENEVA   (Switzerland)

^ar EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^as UNIVERSITÉ PARIS SACLAY   (France)

^at PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^au NATIONAL INSTITUTES OF HEALTH   (United States)

^av INSTITUTE OF MICROBIOLOGY   (China)

^aw UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

KNOWLEDGE BASED SYSTEMS; MASS SPECTROMETRY;

DATA DRIVEN; HIGH THROUGH-PUT CHARACTERIZATION; KNOWLEDGE BASE; MASS SPECTROMETRY DATA; MS LIBRARIES; NATURAL PRODUCTS; OPEN ACCESS; TANDEM MASS;

SPECTROMETRY;

NATURAL PRODUCT; BIOLOGICAL PRODUCT;

BIOINFORMATICS; BIOTECHNOLOGY; COMMUNITY; DATA ANALYSIS; GLOBAL NATURAL PRODUCTS SOCIAL MOLECULAR NETWORKING; HIGH THROUGHPUT SCREENING; INFORMATION RETRIEVAL; KNOWLEDGE BASE; METABOLOMICS; PRIORITY JOURNAL; REVIEW; TANDEM MASS SPECTROMETRY; CHEMICAL DATABASE; CHEMISTRY; CLASSIFICATION; DATABASE MANAGEMENT SYSTEM; INFORMATION DISSEMINATION; INFORMATION PROCESSING; INTERNATIONAL COOPERATION; MASS SPECTROMETRY; PROCEDURES; STATISTICS AND NUMERICAL DATA;

BIOLOGICAL PRODUCTS; DATA CURATION; DATABASE MANAGEMENT SYSTEMS; DATABASES, CHEMICAL; INFORMATION DISSEMINATION; INFORMATION STORAGE AND RETRIEVAL; INTERNATIONALITY; MASS SPECTROMETRY;

EID: 84981297901     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3597     Document Type: Review

References (56)

1. Bouslimani, A., Sanchez, L.M., Garg, N. & Dorrestein, P.C. Mass spectrometry of natural products: current, emerging and future technologies. Nat. Prod. Rep. 31, 718-729 (2014).
2. Dictionary of Natural Products http://dnp.chemnetbase.com/ (2013).
3. Laatsch, H. AntiBase 2012: The Natural Compound Identifiers (Wiley-VCH, 2011).
4. Blunt, J. & Munro, M. MarinLit: a database of the marine natural products literature http://pubs.rsc.org/marinlit/ (Department Chem. Univ. Canterbury, Canterbury, New Zealand) (2003).
5. Hisayuki, H. et al. MassBank: a public repository for sharing mass spectral data for life sciences. J. Mass Spectrom. 45, 703-714 (2010).
6. Smith, C.A. et al. METLIN: a metabolite mass spectral database. Ther. Drug Monit. 27, 747-751 (2005).
7. mzCloud: advanced mass spectral database https://www.mzcloud.org/.
8. Sawada, Y. et al. RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database. Phytochemistry 82, 38-44 (2012).
9. Benson, D.A. et al. GenBank. Nucleic Acids Res. 41, D36-D42 (2013).
10. Magrane, M. & UniProt Consortium. UniProt Knowledgebase: a hub of integrated protein data. Database 2011, bar009 (2011).
11. Lang, G. et al. Evolving trends in the dereplication of natural product extracts: new methodology for rapid, small-scale investigation of natural product extracts. J. Nat. Prod. 71, 1595-1599 (2008).
12. Ito, T. & Masubuchi, M. Dereplication of microbial extracts and related analytical technologies. J. Antibiot. (Tokyo) 67, 353-360 (2014).
13. Little, J.L., Williams, A.J., Pshenichnov, A. & Tkachenko, V. Identification of "known unknowns" utilizing accurate mass data and ChemSpider. J. Am. Soc. Mass Spectrom. 23, 179-185 (2012).
14. Moree, W.J. et al. Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proc. Natl. Acad. Sci. USA 109, 13811-13816 (2012).
15. Watrous, J. et al. Mass spectral molecular networking of living microbial colonies. Proc. Natl. Acad. Sci. USA 109, E1743-E1752 (2012).
16. Nguyen, D.D. et al. MS/MS networking guided analysis of molecule and gene cluster families. Proc. Natl. Acad. Sci. USA 110, E2611-E2620 (2013).
17. Sidebottom, A.M., Johnson, A.R., Karty, J.A., Trader, D.J. & Carlson, E.E. Integrated metabolomics approach facilitates discovery of an unpredicted natural product suite from Streptomyces coelicolor M145. A.C.S. Chem. Biol. 8, 2009-2016 (2013).
18. Vizcaino, M.I., Engel, P., Trautman, E. & Crawford, J.M. Comparative metabolomics and structural characterizations illuminate colibactin pathway-dependent small molecules. J. Am. Chem. Soc. 136, 9244-9247 (2014).
19. Wilson, M.C. et al. An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506, 58-62 (2014).
20. Engel, P., Vizcaino, M.I. & Crawford, J.M. Gut symbionts from distinct hosts exhibit genotoxic activity via divergent colibactin biosynthesis pathways. Appl. Environ. Microbiol. 81, 1502-1512 (2015).
21. Yang, J.Y. et al. Molecular networking as a dereplication strategy. J. Nat. Prod. 76, 1686-1699 (2013).
22. The National Institute of Standards and Technology. NIST standard reference database 1A http://www.nist.gov/srd/nist1a.cfm.
23. Pruitt, K.D., Tatusova, T., Brown, G.R. & Maglott, D.R. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 40, D130-D135 (2012).
24. Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45-48 (2000).
25. Bairoch, A. et al. The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, D154-D159 (2005).
26. Kersten, R.D. et al. Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules. Proc. Natl. Acad. Sci. USA 110, E4407-E4416 (2013).
27. Guthals, A., Watrous, J.D., Dorrestein, P.C. & Bandeira, N. The spectral networks paradigm in high throughput mass spectrometry. Mol. Biosyst. 8, 2535-2544 (2012).
28. Mascuch, S.J. et al. Direct detection of fungal siderophores on bats with white-nose syndrome via fluorescence microscopy-guided ambient ionization mass spectrometry. PLoS One 10, e0119668 (2015).
29. Bandeira, N., Tsur, D., Frank, A. & Pevzner, P. Protein identification by spectral networks analysis. Proc. Natl. Acad. Sci. USA 104, 6140-6145 (2007).
30. Winnikoff, J.R., Glukhov, E., Watrous, J., Dorrestein, P.C. & Gerwick, W.H. Quantitative molecular networking to profile marine cyanobacterial metabolomes. J. Antibiot. (Tokyo) 67, 105-112 (2014).
31. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504 (2003).
32. Kildgaard, S. et al. Accurate dereplication of bioactive secondary metabolites from marine-derived fungi by UHPLC-DAD-QTOFMS and a MS/HRMS library. Mar. Drugs 12, 3681-3705 (2014).
33. Matsuda, F. et al. AtMetExpress development: a phytochemical atlas of Arabidopsis development. Plant Physiol. 152, 566-578 (2010).
34. Haug, K. et al. MetaboLights-an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res. 41, D781-D786 (2013).
35. Martens, L. et al. PRIDE: the proteomics identifications database. Proteomics 5, 3537-3545 (2005).
36. Uchida, K. & Zähner, H. Metabolic products of microorganisms 142. A new antibiotic derinamycin, inhibitor of DNA and RNA synthesis. J. Antibiot. (Tokyo) 28, 266-273 (1975).
37. Liu, W.-T. et al. MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus. J. Antibiot. (Tokyo) 67, 99-104 (2014).
38. Marfey, P. Determination of D-amino acids. II. Use of a bifunctional reagent, 1,5-difluoro-2,4-dinitrobenzene. Carlsberg Res. Commun. 49, 591-596 (1984).
39. Nonejuie, P., Burkart, M., Pogliano, K. & Pogliano, J. Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules. Proc. Natl. Acad. Sci. USA 110, 16169-16174 (2013).
40. Lamsa, A., Liu, W.T., Dorrestein, P.C. & Pogliano, K. The Bacillus subtilis cannibalism toxin SDP collapses the proton motive force and induces autolysis. Mol. Microbiol. 84, 486-500 (2012).
41. Purves, K. et al. Using molecular networking for microbial secondary metabolite bioprospecting. Metabolites 6, 2 (2016).
42. Bertin, M.J. et al. Spongosine production by a Vibrio harveyi strain associated with the sponge Tectitethya crypta. J. Nat. Prod. 78, 493-499 (2015).
43. Boudreau, P.D. et al. Expanding the described metabolome of the marine cyanobacterium Moorea producens JHB through orthogonal natural products workflows. PLoS One 10, e0133297 (2015).
44. Kleigrewe, K. et al. Combining mass spectrometric metabolic profiling with genomic analysis: a powerful approach for discovering natural products from cyanobacteria. J. Nat. Prod. 78, 1671-1682 (2015).
45. Duncan, K.R. et al. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. Chem. Biol. 22, 460-471 (2015).
46. Vizcaino, M.I. & Crawford, J.M. The colibactin warhead crosslinks DNA. Nat. Chem. 7, 411-417 (2015).
47. Klitgaard, A., Nielsen, J.B., Frandsen, R.J.N., Andersen, M.R. & Nielsen, K.F. Combining stable isotope labeling and molecular networking for biosynthetic pathway characterization. Anal. Chem. 87, 6520-6526 (2015).
48. Anderton, C.R., Chu, R.K., Tolilć, N., Creissen, A. & Paša-Tolić, L. Utilizing a robotic sprayer for high lateral and mass resolution MALDI FT-ICR MSI of microbial cultures. J. Am. Soc. Mass Spectrom. 27, 556-559 (2016).
49. Liaimer, A. et al. Nostopeptolide plays a governing role during cellular differentiation of the symbiotic cyanobacterium Nostoc punctiforme. Proc. Natl. Acad. Sci. USA 112, 1862-1867 (2015).
50. Liu, Y. et al. Diversity of aquatic pseudomonas species and their activity against the fish pathogenic oomycete saprolegnia. PLoS One 10, e0136241 (2015).
51. He, X. et al. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc. Natl. Acad. Sci. USA 112, 244-249 (2015).
52. Cha, J.-Y. et al. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J. 10, 119-129 (2016).
53. Dührkop, K., Shen, H., Meusel, M., Rousu, J. & Böcker, S. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc. Natl. Acad. Sci. USA 112, 12580-12585 (2015).
54. Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
55. Wishart, D.S. et al. HMDB: The human metabolome database. Nucleic Acids Res. 35, D521-D526 (2007).
56. Sud, M. et al. Metabolomics Workbench: an international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res. 44, D463-D470 (2016).