I tried to isolate pr-FMN from UbiD like enzyme and verify it via UPLC and Mass spectrometry. The results obtained from MS shows detection of right mass but UPLC spectrum tell another story. How can I identify compound just with mass if it’s not prFMN?
your guidance will be highly appreciated.
Different compounds can have the same mass, of course. To get further elucidation, you could try additional MS techniques, such as MS-MS or exact mass measurement. MS-MS breaks the molecule down into smaller pieces, the masses of which can tell you more about the structure. Exact mass gives you the mass to 4 decimal places, which allows you to narrow down the possible chemical formulas.
UPLC spectrum?... Did you mean UPLC chromatogram or LC-UV spectrum/spectral view?
If you mean chromatogram and resulting different retention times with the same masses, these may be the isomeric variants of the same molecules. This can be clarified by the use of a high-resolution power of the mass spec. High-resolution m/z values (say 40.000 and above FWHMs) can confirm if these are probably the isomeric species.
If you are meaning UV spectral shift differences (distinct UV max absorption wavelengths) but the same masses, probably they are different molecules. You can use the abovementioned second option if you did not apply before.
Alternatively MS/MS and MS to the n experiments would be more beneficial to discriminate the molecules. EAD, CID, HCD, UVPD, and ETD are the orthogonal approaches that can also be used for molecular structure elucidation.
Good luck,
İEA
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