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Molecular Networking as a Dereplication Strategy

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Yang, Jane Y., Sanchez, Laura M., Rath, Christopher M., Liu, Xueting, Boudreau, Paul D., Bruns, Nicole, Glukhov, Evgenia, Wodtke, Anne, de Felicio, Rafael, Fenner, Amanda, Wong, Weng Ruh, Linington, Roger G., Zhang, Lixin, Debonsi, Hosana M., Gerwick, William H., Dorrestein, Pieter C.·2013·Journal of Natural Products

DOI 10.1021/np400413s

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Abstract

A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This approach can accommodate different ionization platforms, enabling cross correlations of MS/MS data from ambient ionization, direct infusion, and LC-based methods. Molecular networking not only dereplicates known molecules from complex mixtures, it also captures related analogues, a challenge for many other dereplication strategies. To illustrate its utility as a dereplication tool, we apply mass spectrometry-based molecular networking to a diverse array of marine and terrestrial microbial samples, illustrating the dereplication of 58 molecules including analogues.

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Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L., & Ideker, T. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq675 · Cited by 4,830
Natural products as sources of new drugs over the 30 years from 1981 to 2010
Newman, D. J., & Cragg, G. M. (2012) · Journal of Natural Products · doi:10.1021/np200906s · Cited by 4,687
GenBank
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1195 · Cited by 3,261
HMDB 3.0—The Human Metabolome Database in 2013
Wishart, D. S., Jewison, T., Guo, A. C., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1065 · Cited by 2,845
MassBank: a public repository for sharing mass spectral data for life sciences
Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., et al. (2010) · Journal of Mass Spectrometry · doi:10.1002/jms.1777 · Cited by 2,529
Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., & Hunt, D. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402700101 · Cited by 2,370
METLIN—a metabolite mass spectral database
Smith, C. A., Maille, G. O., Want, E. J., Qin, C., Trauger, S. A., Brandon, T. R., Custodio, D. E., Abagyan, R., & Siuzdak, G. (2005) · Therapeutic Drug Monitoring · doi:10.1097/01.ftd.0000179845.53213.39 · Cited by 2,226
Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process
Zubarev, R. A., Kelleher, N. L., & McLafferty, F. W. (1998) · Journal of the American Chemical Society · doi:10.1021/ja973478k · Cited by 1,881
LMSD: LIPID MAPS structure database
Sud, M., Fahy, E., Cotter, D., Brown, A., Dennis, E. A., Glass, C. K., Merrill, A. H., Murphy, R. C., Raetz, C. R. H., Russell, D. W., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl838 · Cited by 1,375
Quinolone signaling in the cell-to-cell communication system of Pseudomonas aeruginosa
Pesci, E. C., Milbank, J. B. J., Pearson, J. P., McKnight, S., Kende, A. S., Greenberg, E. P., & Iglewski, B. H. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.20.11229 · Cited by 1,113
Mass spectral molecular networking of living microbial colonies
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., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203689109 · Cited by 971
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Arima, K., Kakinuma, A., & Tamura, G. (1968) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(68)90503-2 · Cited by 908
Infrared Multiphoton Dissociation of Large Multiply Charged Ions for Biomolecule Sequencing
Little, D. P., Speir, J. P., Senko, M. W., O'Connor, P. B., & McLafferty, F. W. (1994) · Analytical Chemistry · doi:10.1021/ac00090a004 · Cited by 753
Chemical Ionization Mass Spectrometry. I. General Introduction
Munson, M. S. B., & Field, F. H. (1966) · Journal of the American Chemical Society · doi:10.1021/ja00964a001 · Cited by 749
Multidimensional Drug Profiling By Automated Microscopy
Perlman, Z. E., Slack, M. D., Feng, Y., Mitchison, T. J., Wu, L. F., & Altschuler, S. J. (2004) · Science · doi:10.1126/science.1100709 · Cited by 660
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Luesch, H., Yoshida, W. Y., Moore, R. E., Paul, V. J., & Corbett, T. H. (2001) · Journal of the American Chemical Society · doi:10.1021/ja010453j · Cited by 373
Genotype-phenotype correlation in 1,507 families with congenital adrenal hyperplasia owing to 21-hydroxylase deficiency
New, M. I., Abraham, M., Gonzalez, B., Dumic, M., Razzaghy-Azar, M., Chitayat, D., Sun, L., Zaidi, M., Wilson, R. C., & Yuen, T. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1300057110 · Cited by 365
Ambient ionization mass spectrometry: A tutorial
Huang, M.-Z., Cheng, S.-C., Cho, Y.-T., & Shiea, J. (2011) · Analytica Chimica Acta · doi:10.1016/j.aca.2011.06.017 · Cited by 320
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Bister, B., Bischoff, D., Ströbele, M., Riedlinger, J., Reicke, A., Wolter, F., Bull, A. T., Zähner, H., Fiedler, H., & Süssmuth, R. D. (2004) · Angewandte Chemie International Edition · doi:10.1002/anie.200353160 · Cited by 309
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Moree, W. J., Phelan, V. V., Wu, C.-H., Bandeira, N., Cornett, D. S., Duggan, B. M., & Dorrestein, P. C. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1206855109 · Cited by 239
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Luesch, H. (2002) · Bioorganic & Medicinal Chemistry · doi:10.1016/s0968-0896(02)00014-7 · Cited by 165
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van der Hooft, J. J. J., de Vos, R. C. H., Ridder, L., Vervoort, J., & Bino, R. J. (2013) · Metabolomics · doi:10.1007/s11306-013-0519-8 · Cited by 46
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See all 607

Authors: 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.
Venue: Journal of Natural Products
Publisher: American Chemical Society (ACS)
Published: 2013-09-11
Volume: 76
Issue: 9
Pages: 1686-1699
ISSN: 0163-3864 (ISSN-L)
1520-6025
DOI: 10.1021/np400413s
OpenAlex: W1966156878
Cited by: 607
References: 53
FWCI: 14.13
Type: journal article
Language: en
Open access: green

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Molecular Networking as a Dereplication Strategy

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