I would be grateful if you could please indicate public libraries used for the identification of natural products produced by bacterial using LC/MS/MS data and/or HPLC DAD analysis
Dear Luciano,
If you have LC-MS/MS data (tandem MS) I would recommend to use the GNPS platform (https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp ) as a first step to identify metabolites in your bacterial extracts. There you can perform a high-throughput dereplication based on MS/MS comparisons with the GPNS library, in addition to molecular networks for find putative analogues. I suggest you to read the documentation first (https://ccms-ucsd.github.io/GNPSDocumentation/librarysearch/) to have a broader idea. After you have done the library search, I suggest you to manually check each hit and compare the monoisotopic ion masses and fragmentation patterns to discard possible mismatches (check also that the data in the library and the data you uploaded were obtained in the same ionization mode). An additional database I use for dereplication based on MS/MS is mzcloud (https://www.mzcloud.org/), which has the advantage of being constantly curated and for each metabolite there are several MS spectra obtained with different ionization energies.
You can also use the Dictionary of Natural Products (http://dnp.chemnetbase.com/faces/chemical/ChemicalSearch.xhtml)
and MassBank (http://www.massbank.jp/) for dereplication based only on monoisotopic mass comparisons (No MS/MS) of high-resolution MS data.
Kind regards,
Dear Luciano,
If you have LC-MS/MS data (tandem MS) I would recommend to use the GNPS platform (https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp ) as a first step to identify metabolites in your bacterial extracts. There you can perform a high-throughput dereplication based on MS/MS comparisons with the GPNS library, in addition to molecular networks for find putative analogues. I suggest you to read the documentation first (https://ccms-ucsd.github.io/GNPSDocumentation/librarysearch/) to have a broader idea. After you have done the library search, I suggest you to manually check each hit and compare the monoisotopic ion masses and fragmentation patterns to discard possible mismatches (check also that the data in the library and the data you uploaded were obtained in the same ionization mode). An additional database I use for dereplication based on MS/MS is mzcloud (https://www.mzcloud.org/), which has the advantage of being constantly curated and for each metabolite there are several MS spectra obtained with different ionization energies.
You can also use the Dictionary of Natural Products (http://dnp.chemnetbase.com/faces/chemical/ChemicalSearch.xhtml)
and MassBank (http://www.massbank.jp/) for dereplication based only on monoisotopic mass comparisons (No MS/MS) of high-resolution MS data.
Kind regards,
Please look at the following below links which may help you in your analysis:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306935/pdf/marinedrugs-13-00249.pdf
https://www.intechopen.com/books/applications-from-engineering-with-matlab-concepts/small-molecule-lc-ms-ms-fragmentation-data-analysis-and-application-to-siderophore-identification
Thanks
Hi, I think you can apply MS data bases for LC MS MS such as Metlin, Metfrag, CFMID, MassBank, MzMine, GNPS,etc you can easily get the link via Google.
Best regards
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