The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication
Open accessAbstract
Dereplication represents a key step for rapidly identifying known secondary metabolites in complex biological matrices. In this context, liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is increasingly used and, via untargeted data-dependent MS/MS experiments, massive amounts of detailed information on the chemical composition of crude extracts can be generated. An efficient exploitation of such data sets requires automated data treatment and access to dedicated fragmentation databases. Various novel bioinformatics approaches such as molecular networking (MN) and in-silico fragmentation tools have emerged recently and provide new perspective for early metabolite identification in natural products (NPs) research. Here we propose an innovative dereplication strategy based on the combination of MN with an extensive in-silico MS/MS fragmentation database of NPs. Using two case studies, we demonstrate that this combined approach offers a powerful tool to navigate through the chemistry of complex NPs extracts, dereplicate metabolites, and annotate analogues of database entries.
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
The re-emergence of natural products for drug discovery in the genomics era
Harvey, A. L., Edrada-Ebel, R., & Quinn, R. J. (2015) · Nature Reviews Drug Discovery · doi:10.1038/nrd4510 · Cited by 2,572
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
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
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R., Lee, S. Y., Fischbach, M. A., Müller, R., Wohlleben, W., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv437 · Cited by 1,868
Kind, T., & Fiehn, O. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-105 · Cited by 1,201
Searching molecular structure databases with tandem mass spectra using CSI:FingerID
Dührkop, K., Shen, H., Meusel, M., Rousu, J., & Böcker, S. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1509788112 · Cited by 1,190
LipidBlast in silico tandem mass spectrometry database for lipid identification
Kind, T., Liu, K.-H., Lee, D. Y., DeFelice, B., Meissen, J. K., & Fiehn, O. (2013) · Nature Methods · doi:10.1038/nmeth.2551 · Cited by 981
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
Kind, T., & Fiehn, O. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-234 · Cited by 637
Current 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
Self-citation
Cited by
Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra
Dührkop, K., Nothias, L.-F., Fleischauer, M., Reher, R., Ludwig, M., Hoffmann, M. A., Petras, D., Gerwick, W. H., Rousu, J., Dorrestein, P. C., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0740-8 · Cited by 860
Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics
Blaženović, I., Kind, T., Ji, J., & Fiehn, O. (2018) · Metabolites · doi:10.3390/metabo8020031 · Cited by 757
Nothias, L.-F., Nothias-Esposito, M., da Silva, R., Wang, M., Protsyuk, I., Zhang, Z., Sarvepalli, A., Leyssen, P., Touboul, D., Costa, J., et al. (2018) · Journal of Natural Products · doi:10.1021/acs.jnatprod.7b00737 · Cited by 433
Self-citationVaou, N., Stavropoulou, E., Voidarou, C. (., Tsakris, Z., Rozos, G., Tsigalou, C., & Bezirtzoglou, E. (2022) · Antibiotics · doi:10.3390/antibiotics11081014 · Cited by 406
Propagating annotations of molecular networks using in silico fragmentation
da Silva, R. R., Wang, M., Nothias, L.-F., van der Hooft, J. J. J., Caraballo-Rodríguez, A. M., Fox, E., Balunas, M. J., Klassen, J. L., Lopes, N. P., & Dorrestein, P. C. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006089 · Cited by 363
Metadata
- Authors
- Allard, P.-M., Péresse, T., Bisson, J., Gindro, K., Marcourt, L., Pham, V. C., Roussi, F., Litaudon, M., & Wolfender, J.-L.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2016-03-01
- Volume
- 88
- Issue
- 6
- Pages
- 3317-3323
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- OpenAlex
- W2283606770
- Cited by
- 431
- References
- 37
- FWCI
- 18.36
- 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: Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication. https://app.cochat.ai/papers/10.1021/acs.analchem.5b04804
- The paper
- Allard, P.-M., Péresse, T., Bisson, J., Gindro, K., Marcourt, L., Pham, V. C., Roussi, F., Litaudon, M., & Wolfender, J.-L. (2016). Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication. Analytical Chemistry. https://doi.org/10.1021/acs.analchem.5b04804
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.
