I'm doing a drug discovery project using Streptomyces. Apart from StreptomeDB, what HPLC-MS databases are good to search to see if I have a new compound? Thanks!
If you are using MS/MS, you can use molecular networking or use the GnPs website: https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp
If however you are doing HPLC-MS, you have to go through multiple de-replication step; use Antimarin, Marinlit, both are commercial though, yet most widely used in NP drug discovery labs. Attached is an image of all DBs used.
Best of luck.
Thanks to both of you. Quick followup question - does anyone go through their peaks manually, or is it all done by automated dereplication programmes where you just input the spectra (sorry if it's a basic question, my university hasn't done this much before!)?
Don't be sorry for the type of question, we were all at your stage at one point!
So in our lab, our HPLC-MS is a Shimadzu and it uses the software LC-Solutions which uses its own UV database to check if the UV of a certain peak is similar to a known compound. Perhaps you have a different instrument with a different software, but mainly it is the same idea. One you look at your UV chromatogram, you can click on a peak and the software will give you the top match(s) for each UV peak you click; although even if you get a hit it doesn't necessarily mean that it is that molecule, but it could have a similar structure. UV can give you information about the conjugation of your molecule (as in how many double bond and/or ring structure your molecule has). For MS however, you have to look at your peak of interest manually and input the parent mass into Antimarin or even Chembl shared above by Pavel or any other database (we usually use a combination of Antimarin and Pubchem. So if you have multiple peaks in your run, you have to consider each and de-replicate each peak by UV, MS and even MS/MS if you can get access to an HPLC-MS/MS. See this link for how to de-replicate using MS databases:
https://www.researchgate.net/post/How_do_I_find_molecular_formulas_from_a_mass_spectrum
Feel free to ask anymore questions, basic or not!
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