The DOI matches its Crossref record; 53 of the 53 references it cites were found in a registry or an index.
Molecular Networking as a Dereplication Strategy
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cytoscape 2.8: new features for data integration and network visualization
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
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
Cited by
Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3597 · Cited by 4,629
Self-citationGut microbiome structure and metabolic activity in inflammatory bowel disease
Franzosa, E. A., Sirota-Madi, A., Avila-Pacheco, J., Fornelos, N., Haiser, H. J., Reinker, S., Vatanen, T., Hall, A. B., Mallick, H., McIver, L. J., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0306-4 · Cited by 1,995
Feature-based molecular networking in the GNPS analysis environment
Nothias, L.-F., Petras, D., Schmid, R., Dührkop, K., Rainer, J., Sarvepalli, A., Protsyuk, I., Ernst, M., Tsugawa, H., Fleischauer, M., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0933-6 · Cited by 1,634
Self-citationAmerican Gut: an Open Platform for Citizen-Science Microbiome Research
McDonalda, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., et al. (2018) · doi:10.1101/277970 · Cited by 878
Self-citationCurrent approaches and challenges for the metabolite profiling of complex natural extracts
Wolfender, J.-L., Marti, G., Thomas, A., & Bertrand, S. (2015) · Journal of Chromatography A · doi:10.1016/j.chroma.2014.10.091 · Cited by 635
Metadata
- 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
- OpenAlex
- W1966156878
- Cited by
- 607
- References
- 53
- FWCI
- 14.13
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Molecular Networking as a Dereplication Strategy. https://app.cochat.ai/papers/10.1021/np400413s
- The paper
- 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. (2013). Molecular Networking as a Dereplication Strategy. Journal of Natural Products. https://doi.org/10.1021/np400413s
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
