With the active fractions from Si-gel CC, I did high resolution LC-MS/MS experiments and got the spectrum. However, I haven't find any reference of purifying the compounds from the same sample. Could anyone suggest me how to search the database with MS spectrum to get the chemical structure?
Or which database can I sear for my purposes?
If it is a compound you synthesized, you should already have an idea of it's mass. As mentioned above by Dr. Boczkaj, look for adducts (from your HPLC solvents) and different charge carriers (sodium or potassium replacing a proton so the detected ion is [M+Na] or [M+K], for example). Solvent adducts would appear as [M+MeOH+H] or [M+ACN+H]. Also, look for loss of various groups from your [M+H] mass such as ammonia (from primary amines) or water (alcohols). Look for loss of CO2 from carboxylic acids in [M-H].
We are assuming ESI or APCI in the discussion above. If doing EI, you may find McLafferty rearrangements.
This DataBase is entirely about MS spectrums, you might find it useful, you are able to upload the data of your spectrums on a .txt file. I dont know if is just occuring on my country, but they have beeing having some issues with creating new accounts, if it also happens to you, you can check it later https://metlin.scripps.edu/landing_page.php?pgcontent=mainPage
On the other hand, NIST and SDBS are the most common databases, however you might need to have any clue about the metabolites you are searching for these to be useful.
You can use the databases suggested by Santiago, but remember, that the molecular ion can be "hidden"/combined with some adducts with compounds present in your eluent.
regards,
G
If it is a compound you synthesized, you should already have an idea of it's mass. As mentioned above by Dr. Boczkaj, look for adducts (from your HPLC solvents) and different charge carriers (sodium or potassium replacing a proton so the detected ion is [M+Na] or [M+K], for example). Solvent adducts would appear as [M+MeOH+H] or [M+ACN+H]. Also, look for loss of various groups from your [M+H] mass such as ammonia (from primary amines) or water (alcohols). Look for loss of CO2 from carboxylic acids in [M-H].
We are assuming ESI or APCI in the discussion above. If doing EI, you may find McLafferty rearrangements.
If you synthesized your target compound, you have littile idea about what type of groups are present there. But if you dont know, I think you should do MS/MS of this reaction mixture. For further queries regarding your spectra you can see following link-
http://www.dcne.ugto.mx/Contenido/MaterialDidactico/amezquita/Analitica4/Silverstein%20-%20Spectrometric%20Identification%20of%20Organic%20Compounds%207th%20ed.pdf
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