Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication

Analytical Chemistry

Volumn 88, Issue 6, 2016, Pages 3317-3323

  Allard, Pierre Marie ^a   Péresse, Tiphaine ^b   Bisson, Jonathan ^c   Gindro, Katia ^d   Marcourt, Laurence ^a   Pham, Van Cuong ^e   Roussi, Fanny ^b   Litaudon, Marc ^b   Wolfender, Jean Luc ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b CNRS   (France)

^c UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^d AGROSCOPE   (Switzerland)

^e GRADUATE UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Viet Nam)

Author keywords

[No Author keywords available]

Indexed keywords

AIR NAVIGATION; BIOINFORMATICS; BIOMOLECULES; CHROMATOGRAPHY; DATABASE SYSTEMS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY;

BIOLOGICAL MATRIXES; CHEMICAL COMPOSITIONS; DATA DEPENDENT MS/MS; HIGH RESOLUTION MASS SPECTROMETRY; METABOLITE IDENTIFICATION; MS/MS FRAGMENTATION; NATURAL PRODUCTS; SECONDARY METABOLITES;

METABOLITES;

BIOLOGICAL PRODUCT;

CHEMISTRY; COMPUTER SIMULATION; LIQUID CHROMATOGRAPHY; PROCEDURES; TANDEM MASS SPECTROMETRY;

BIOLOGICAL PRODUCTS; CHROMATOGRAPHY, LIQUID; COMPUTER SIMULATION; TANDEM MASS SPECTROMETRY;

EID: 84961218887     PISSN: 00032700     EISSN: 15206882     Source Type: Journal    
DOI: 10.1021/acs.analchem.5b04804     Document Type: Article

References (51)

1. Harvey, A. L.; Edrada-Ebel, R.; Quinn, R. J. Nat. Rev. Drug Discovery 2015, 14, 111-129 10.1038/nrd4510
2. Wishart, D. S. Bioanalysis 2011, 3, 1769-1782 10.4155/bio.11.155
3. Gaudêncio, S. P.; Pereira, F. Nat. Prod. Rep. 2015, 32, 779-810 10.1039/C4NP00134F
4. Wolfender, J.-L.; Marti, G.; Thomas, A.; Bertrand, S. J. Chromatogr. A 2015, 1382, 136-164 10.1016/j.chroma.2014.10.091
5. Kind, T.; Fiehn, O. BMC Bioinf. 2007, 8, 105 10.1186/1471-2105-8-105
6. Kind, T.; Fiehn, O. BMC Bioinf. 2006, 7, 234 10.1186/1471-2105-7-234
7. Nielsen, K. F.; Larsen, T. O. Front. Microbiol. 2015, 6, 1-15 10.3389/fmicb.2015.00071
8. Ridder, L.; van der Hooft, J. J. J.; Verhoeven, S.; de Vos, R. C. H.; Vervoort, J.; Bino, R. J. Anal. Chem. 2014, 86, 4767-4774 10.1021/ac403875b
9. van der Hooft, J. J. J.; Vervoort, J.; Bino, R. J.; de Vos, R. C. H. Metabolomics 2012, 8, 691-703 10.1007/s11306-011-0363-7
10. Watrous, J.; Roach, P.; Alexandrov, T.; Heath, B. S.; Yang, J. Y.; Kersten, R. D.; van der Voort, M.; Pogliano, K.; Gross, H.; Raaijmakers, J. M.; Moore, B. S.; Laskin, J.; Bandeira, N.; Dorrestein, P. C. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, E1743-E1752 10.1073/pnas.1203689109
11. Traxler, M. F.; Kolter, R. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 10128-10129 10.1073/pnas.1207725109
12. Yang, J. Y.; Sanchez, L. M.; Rath, C. M.; Liu, X.; Boudreau, P. D.; Bruns, N.; Glukhov, E.; Wodtke, A.; de Felicio, R.; Fenner, A.; Wong, W. R.; Linington, R. G.; Zhang, L.; Debonsi, H. M.; Gerwick, W. H.; Dorrestein, P. C. J. Nat. Prod. 2013, 76, 1686-1699 10.1021/np400413s
13. Kleigrewe, K.; Almaliti, J.; Tian, I. Y.; Kinnel, R. B.; Korobeynikov, A.; Monroe, E. a.; Duggan, B. M.; Di Marzo, V.; Sherman, D. H.; Dorrestein, P. C.; Gerwick, L.; Gerwick, W. H. J. Nat. Prod. 2015, 78, 1671-1682 10.1021/acs.jnatprod.5b00301
14. Brito, Â.; Gaifem, J.; Ramos, V.; Glukhov, E.; Dorrestein, P. C.; Gerwick, W. H.; Vasconcelos, V. M.; Mendes, M. V.; Tamagnini, P. Algal Res. 2015, 9, 218-226 10.1016/j.algal.2015.03.016
15. Duncan, K. R.; Crüsemann, M.; Lechner, A.; Sarkar, A.; Li, J.; Ziemert, N.; Wang, M.; Bandeira, N.; Moore, B. S.; Dorrestein, P. C.; Jensen, P. R. Chem. Biol. 2015, 22, 460-471 10.1016/j.chembiol.2015.03.010
16. Klitgaard, A.; Nielsen, J. B.; Frandsen, R. J. N.; Andersen, M. R.; Nielsen, K. F. Anal. Chem. 2015, 87, 6520-6526 10.1021/acs.analchem.5b01934
17. Mohimani, H.; Pevzner, P. A. Nat. Prod. Rep. 2016, 33, 73-86 10.1039/C5NP00050E
18. Horai, H.; Arita, M.; Kanaya, S.; Nihei, Y.; Ikeda, T.; Suwa, K.; Ojima, Y.; Tanaka, K.; Tanaka, S.; Aoshima, K.; Oda, Y.; Kakazu, Y.; Kusano, M.; Tohge, T.; Matsuda, F.; Sawada, Y.; Hirai, M. Y.; Nakanishi, H.; Ikeda, K.; Akimoto, N.; Maoka, T.; Takahashi, H.; Ara, T.; Sakurai, N.; Suzuki, H.; Shibata, D.; Neumann, S.; Iida, T.; Tanaka, K.; Funatsu, K.; Matsuura, F.; Soga, T.; Taguchi, R.; Saito, K.; Nishioka, T. J. Mass Spectrom. 2010, 45, 703-714 10.1002/jms.1777
19. Smith, C. A.; O'Maille, G.; Want, E. J.; Qin, C.; Trauger, S. A.; Brandon, T. R.; Custodio, D. E.; Abagyan, R.; Siuzdak, G. Ther. Drug Monit. 2005, 27, 747-751 10.1097/01.ftd.0000179845.53213.39
20. Sawada, Y.; Nakabayashi, R.; Yamada, Y.; Suzuki, M.; Sato, M.; Sakata, A.; Akiyama, K.; Sakurai, T.; Matsuda, F.; Aoki, T.; Hirai, M. Y.; Saito, K. Phytochemistry 2012, 82, 38-45 10.1016/j.phytochem.2012.07.007
21. The National Institute of Standards and Technology. NIST. http://www.nist.gov/srd/nist1a.cfm (accessed Dec 16, 2015).
22. GNPS http://gnps.ucsd.edu/ (accessed Dec 16, 2015).
23. Kind, T.; Liu, K.-H.; Lee, D. Y.; DeFelice, B.; Meissen, J. K.; Fiehn, O. Nat. Methods 2013, 10, 755-758 10.1038/nmeth.2551
24. Mander, L. N.; Liu, H.-W. Comprehensive Natural Products II: Chemistry and Biology; Elsevier: Amsterdam, 2010.
25. Hufsky, F.; Scheubert, K.; Böcker, S. Nat. Prod. Rep. 2014, 31, 807 10.1039/c3np70101h
26. Dührkop, K.; Shen, H.; Meusel, M.; Rousu, J.; Böcker, S. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 12580-12585 10.1073/pnas.1509788112
27. Huan, T.; Tang, C.; Li, R.; Shi, Y.; Lin, G.; Li, L. Anal. Chem. 2015, 87, 10619-10626 10.1021/acs.analchem.5b03126
28. da Silva, R. R.; Dorrestein, P. C.; Quinn, R. a. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 12549-12550 10.1073/pnas.1516878112
29. Allen, F.; Greiner, R.; Wishart, D. Metabolomics 2015, 11, 98-110 10.1007/s11306-014-0676-4
30. Baobab HPC Cluster https://plone.unige.ch/distic/pub/hpc/baobab-en (accessed Dec 16, 2015).
31. Wang, M.; Bandeira, N. J. Proteome Res. 2013, 12, 3944-3951 10.1021/pr400230p
32. Gu, J.; Gui, Y.; Chen, L.; Yuan, G.; Lu, H.-Z.; Xu, X. PLoS One 2013, 8, e62839 10.1371/journal.pone.0062839
33. Thoison, O.; Hnawia, E.; Guiéritte-Voegelein, F.; Sévenet, T. Phytochemistry 1992, 31, 1439-1442 10.1016/0031-9422(92)80315-6
34. Beutler, J. a.; Shoemaker, R. H.; Johnson, T.; Boyd, M. R. J. Nat. Prod. 1998, 61, 1509-1512 10.1021/np980208m
35. Beutler, J.; Jato, J.; Cragg, G.; Boyd, M. Nat. Prod. Lett. 2000, 14, 399-404 10.1080/10575630008043774
36. Turbyville, T. J.; Gürsel, D. B.; Tuskan, R. G.; Walrath, J. C.; Lipschultz, C. a; Lockett, S. J.; Wiemer, D. F.; Beutler, J. a; Reilly, K. M. Mol. Cancer Ther. 2010, 9, 1234-1243 10.1158/1535-7163.MCT-09-0834
37. Audoin, C.; Cocandeau, V.; Thomas, O.; Bruschini, A.; Holderith, S.; Genta-Jouve, G. Metabolites 2014, 4, 421-432 10.3390/metabo4020421
38. Du, L.; Robles, A. J.; King, J. B.; Powell, D. R.; Miller, A. N.; Mooberry, S. L.; Cichewicz, R. H. Angew. Chem., Int. Ed. 2014, 53, 804-809 10.1002/anie.201306549
39. Wang, X.; Sena Filho, J. G.; Hoover, A. R.; King, J. B.; Ellis, T. K.; Powell, D. R.; Cichewicz, R. H. J. Nat. Prod. 2010, 73, 942-948 10.1021/np100142h
40. Fisch, K. M.; Gillaspy, a F.; Gipson, M.; Henrikson, J. C.; Hoover, a R.; Jackson, L.; Najar, F. Z.; Wägele, H.; Cichewicz, R. H. J. Ind. Microbiol. Biotechnol. 2009, 36, 1199-1213 10.1007/s10295-009-0601-4
41. Miller, T. A.; Witter, D. J.; Belvedere, S. Histone Deacetylase Inhibitor Prodrugs. U.S. 2009/0023786A1, 2009.
42. Gediya, L. K.; Chopra, P.; Purushottamachar, P.; Maheshwari, N.; Njar, V. C. O. J. Med. Chem. 2005, 48, 5047-5051 10.1021/jm058214k
43. Makino, M.; Endoh, T.; Ogawa, Y.; Watanabe, K.; Fujimoto, Y. Heterocycles 1998, 48, 1931-1934 10.3987/COM-98-8253
44. Chung, Y.; El-Shazly, M.; Chuang, D.-W.; Hwang, T.; Asai, T.; Oshima, Y.; Ashour, M. L.; Wu, Y.; Chang, F. J. Nat. Prod. 2013, 76, 1260-1266 10.1021/np400143j
45. Miao, F.; Liang, X.; Liu, X.; Ji, N. J. Nat. Prod. 2014, 77, 429-432 10.1021/np401047w
46. Du, L.; King, J. B.; Cichewicz, R. H. J. Nat. Prod. 2014, 77, 2454-2458 10.1021/np500522z
47. Henrikson, J. C.; Ellis, T. K.; King, J. B.; Cichewicz, R. H. J. Nat. Prod. 2011, 74, 1959-1964 10.1021/np200454z
48. Menikarachchi, L. C.; Hill, D. W.; Hamdalla, M. a.; Mandoiu, I. I.; Grant, D. F. J. Chem. Inf. Model. 2013, 53, 2483-2492 10.1021/ci400368v
49. Jeffryes, J. G.; Colastani, R. L.; Elbadawi-Sidhu, M.; Kind, T.; Niehaus, T. D.; Broadbelt, L. J.; Hanson, A. D.; Fiehn, O.; Tyo, K. E. J.; Henry, C. S. J. Cheminf. 2015, 7, 44 10.1186/s13321-015-0087-1
50. Weber, T.; Blin, K.; Duddela, S.; Krug, D.; Kim, H. U.; Bruccoleri, R.; Lee, S. Y.; Fischbach, M. a.; Muller, R.; Wohlleben, W.; Breitling, R.; Takano, E.; Medema, M. H. Nucleic Acids Res. 2015, 43, 237-243 10.1093/nar/gkv437
51. Yadav, G.; Gokhale, R. S.; Mohanty, D. PLoS Comput. Biol. 2009, 5, e1000351 10.1371/journal.pcbi.1000351