I understand that mass spec is widely used to study PTMs like glycosylation of proteins, but how can mass spec determine correct PTM structure of say glycosylation if two glycan structures have the same mass but different arrangement (i.e. isobaric)? Also, how can mass spec determine the difference between structural isomers?
I am not a MassSpec expert but this is what I understand from my spectroscopy basics:
In tandem MS (MS-MS), the ionized analyte generally undergoes or made to undergo fragmentation (breaking up into smaller ions). Fragmentation allows you to study finer details. It is also essential for de-novo peptide sequencing. Different fragmentation techniques, such as Collision Induced Dissociation (CID) or Photofragmentation, yield different kinds of secondary ions.
You can intuitively understand that Fragmentation of structural isomers will yield different kinds of secondary ions (using the same fragmentation technique). The choice of fragmentation technique depends on the molecular nature of the analyte. In the article that I mentioned previously, they use laser induced photofragmentation to dissociate glycan-ions.
Even small molecules, which had been classically studied by MassSpec, undergo isomerization after ionization in order to stabilize the ion. Reactions such as reverse-Diels-Adler can also happen. The pattern of reactions would differ between structural isomers. For basics you can refer to a book on Spectroscopic techniques by Silverstein