Kale, N. S. et al. MetaboLights: an analog-access database repository for metabolomics data. Curr. Protoc. Bioinformatics 53, 14–13 (2016).
Article
Google Scholar
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).
Article
CAS
PubMed
Google Scholar
Wang, M. et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat. Biotechnol. 34, 828–837 (2016).
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang, M. et al. Mass spectrometry searches using MASST. Nat. Biotechnol. 38, 23–26 (2020).
Article
PubMed
PubMed Central
Google Scholar
Courraud, J., Ernst, M., Svane Laursen, S., Hougaard, D. M. & Cohen, A. S. Studying autism using untargeted metabolomics in newborn screening samples. J. Mol. Neurosci. 71, 1378–1393 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Ernst, M. et al. Gestational age-dependent development of the neonatal metabolome. Pediatr. Res. 89, 1396–1404 (2021).
Article
CAS
PubMed
Google Scholar
Frank, A. M. et al. Clustering millions of tandem mass spectra. J. Proteome Res. 7, 113–122 (2008).
Article
CAS
PubMed
Google Scholar
Jarmusch, A. K. et al. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat. Methods 17, 901–904 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Quinn, R. A. et al. Global chemical effects of the microbiome include new bile-acid conjugations. Nature 579, 123–129 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Petras, D. et al. Non-targeted metabolomics enables the prioritization and tracking of anthropogenic pollutants in coastal seawater. Chemosphere 271 (2020).
Kuo, T.-H., Yang, C.-T., Chang, H.-Y., Hsueh, Y.-P. & Hsu, C.-C. Nematode-trapping fungi produce diverse metabolites during predator–prey interaction. Metabolites 10, 117 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Depke, T., Thöming, J. G., Kordes, A., Häussler, S. & Brönstrup, M. Untargeted LC-MS metabolomics differentiates between virulent and avirulent clinical strains of Pseudomonas aeruginosa. Biomolecules 10, 1041 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Eberhard, F. E., Klimpel, S., Guarneri, A. A. & Tobias, N. J. Metabolites as predictive biomarkers for Trypanosoma cruzi exposure in triatomine bugs. Comput. Struct. Biotechnol. J. 19, 3051–3057 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Lybbert, A. C., Williams, J. L., Raghuvanshi, R., Jones, A. D. & Quinn, R. A. Mining public mass spectrometry data to characterize the diversity and ubiquity of P. aeruginosa specialized metabolites. Metabolites 10, 445 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Mohimani, H. et al. Dereplication of peptidic natural products through database search of mass spectra. Nat. Chem. Biol. 13, 30–37 (2017).
Article
CAS
PubMed
Google Scholar
Frank, A. M. et al. Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat. Methods 8, 587–591 (2011).
Article
CAS
PubMed
PubMed Central
Google Scholar
Bandeira, N., Tsur, D., Frank, A. & Pevzner, P. A. Protein identification by spectral networks analysis. Proc. Natl Acad. Sci. USA 104, 6140–6145 (2007).
Article
CAS
PubMed
PubMed Central
Google Scholar
Ramos, A. E. F., Evanno, L., Poupon, E., Champy, P. & Beniddir, M. A. Natural products targeting strategies involving molecular networking: different manners, one goal. Nat. Prod. Rep. 36, 960–980 (2019).
Article
Google Scholar
Kalinski, J.-C. J. et al. Molecular networking reveals two distinct chemotypes in pyrroloiminoquinone-producing Tsitsikamma favus sponges. Marine Drugs 17, 60 (2019).
Article
CAS
PubMed
PubMed Central
Google Scholar
Raheem, D. J., Tawfike, A. F., Abdelmohsen, U. R., Edrada-Ebel, R. & Fitzsimmons-Thoss, V. Application of metabolomics and molecular networking in investigating the chemical profile and antitrypanosomal activity of British bluebells (Hyacinthoides non-scripta). Sci. Rep. 9, 2547 (2019).
Article
PubMed
PubMed Central
Google Scholar
Trautman, E. P., Healy, A. R., Shine, E. E., Herzon, S. B. & Crawford, J. M. Domain-targeted metabolomics delineates the heterocycle assembly steps of colibactin biosynthesis. J. Am. Chem. Soc. 139, 4195–4201 (2017).
Article
CAS
PubMed
PubMed Central
Google Scholar
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).
Article
CAS
PubMed
PubMed Central
Google Scholar
Nguyen, D. D. et al. Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nat. Microbiol. 2, 16197 (2016).
Article
CAS
PubMed
PubMed Central
Google Scholar
Woo, S., Kang, K. B., Kim, J. & Sung, S. H. Molecular networking reveals the chemical diversity of selaginellin derivatives, natural phosphodiesterase-4 inhibitors from Selaginella tamariscina. J. Nat. Prod. 82, 1820–1830 (2019).
Article
CAS
PubMed
Google Scholar
Reginaldo, F. P. S. et al. Molecular networking discloses the chemical diversity of flavonoids and selaginellins in Selaginella convoluta. Planta Med. 87, 113–123 (2021).
Article
CAS
PubMed
Google Scholar
Bittremieux, W. et al. Analog access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Preprint at bioRxiv https://doi.org/10.1101/2022.05.15.490691 (2022).
Schnell, N. et al. Prepeptide sequence of epidermin, a ribosomally synthesized antibiotic with four sulphide-rings. Nature 333, 276–278 (1988).
Article
CAS
PubMed
Google Scholar
Mohr, K. I. et al. Pinensins: the first antifungal lantibiotics. Angew. Chem. Int. Ed. 54, 11254–11258 (2015).
Article
CAS
Google Scholar
Férir, G. et al. The lantibiotic peptide labyrinthopeptin A1 demonstrates broad anti-HIV and anti-HSV activity with potential for microbicidal applications. PLoS ONE 8, e64010 (2013).
Article
PubMed
PubMed Central
Google Scholar
Iorio, M. et al. A glycosylated, labionin-containing lanthipeptide with marked antinociceptive activity. ACS Chem. Biol. 9, 398–404 (2014).
Article
CAS
PubMed
Google Scholar
Arnison, P. G. et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat. Prod. Rep. 30, 108–160 (2013).
Article
CAS
PubMed
PubMed Central
Google Scholar
Frank, A. & Pevzner, P. PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem. 77, 964–973 (2005).
Article
CAS
PubMed
Google Scholar
Walker, M. C. et al. Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family. BMC Genomics 21, 387 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Kodani, S., Lodato, M. A., Durrant, M. C., Picart, F. & Willey, J. M. SapT, a lanthionine-containing peptide involved in aerial hyphae formation in the streptomycetes. Mol. Microbiol. 58, 1368–1380 (2005).
Article
CAS
PubMed
Google Scholar
Ueda, K. et al. AmfS, an extracellular peptidic morphogen in Streptomyces griseus. J. Bacteriol. 184, 1488–1492 (2002).
Article
CAS
PubMed
PubMed Central
Google Scholar
da Silva, R. R., Dorrestein, P. C. & Quinn, R. A. Illuminating the dark matter in metabolomics. Proc. Natl Acad. Sci. USA 112, 12549–12550 (2015).
Article
PubMed
PubMed Central
Google Scholar
Aron, A. T. et al. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat. Protoc. 15, 1954–1991 (2020).
Article
CAS
PubMed
Google Scholar
Nothias, L.-F. et al. Feature-based molecular networking in the GNPS analysis environment. Nat. Methods 17, 905–908 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
van Der Hooft, J. J. et al. Linking genomics and metabolomics to chart specialized metabolic diversity. Chem. Soc. Rev. 49, 3297–3314 (2020).
Article
PubMed
Google Scholar
Yang, J. Y. et al. Molecular networking as a dereplication strategy. J. Nat. Prod. 76, 1686–1699 (2013).
Article
CAS
PubMed
PubMed Central
Google Scholar
Watrous, J. et al. Mass spectral molecular networking of living microbial colonies. Proc. Natl Acad. Sci. USA 109, E1743–E1752 (2012).
Article
CAS
PubMed
PubMed Central
Google Scholar
Ludwig, M., Fleischauer, M., Dührkop, K., Hoffmann, M. A. & Böcker, S. De novo molecular formula annotation and structure elucidation using SIRIUS 4. Methods Mol. Biol. 2104, 185–207 (2020).
Dührkop, K. et al. Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra. Nat. Biotechnol 39, 462–471 (2021).
Article
PubMed
Google Scholar
Mohimani, H., Kim, S. and Pevzner, P. A. A new approach to evaluating statistical significance of spectral identifications. J. Proteome Res. 12, 1560–1568 (2013).
>>> Read full article>>>
Copyright for syndicated content belongs to the linked Source : Nature.com – https://www.nature.com/articles/s41587-023-01985-4
