I did a metabolomic study, where some of my compounds are novel and have high production in one of my mutants. I have its m/z ratio. Can I identify this compound solely based on this ratio? I understand the ratio could be the same for other similar compounds. How do I determine what this compound is? Any help or path would be greatly appreciated.
Dear Sandesh Sharma Pandit
You cannot unequivocally identify a compound solely based on m/z. Potentially many molecules can have the same molecular composition (the higher the molecular weight, the more possibilities). For some compounds, MS/MS measurement combined with the fragmentation of the molecule (induced, for example, by collision with an inert gas) can be helpful. For deeper insight, you probably need NMR or at least HPLC parallel runs for your sample and standard compound (by comparing their retention time).
MS-MS experiments should help narrow down the possibilities. Also, if you can obtain a high-precision mass (i.e. 4 decimal places), you can get some suggestions about the chemical formula.
Nominal mass m/z will give you very little to go on. Accurate Mass at around 1ppm mass accuracy may lead to a small number of possible molecular formulae but each of these could represent millions of different possible chemical structures. A molecular formula might help you search existing databases if you are sure that your metabolite is known. Otherwise, NMR would be my choice. The combination of NMR and accurate mass would be the most likely way to identify the material of interest.
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