Fragmentation Modes of Different Ion Types
Carbohydrates produce a variety of ion types depending on the ionization method used and the structure of the carbohydrate. [M+Na]+ are ubiquitous in MALDI spectra of neutral glycans, but [M+H]+ ions can be formed if there is a site for protonation, as with many derivatized glycans. In negative ion mode, relatively unstable [M-H]- or [M-"H]"- ions are frequently encountered, particularly from glycans containing anionic groups, but more stable ions can be formed by adduction with various anions.
Protonated molecules decompose much more readily than metal-cationized species and yield mainly B- and Y-type glycosidic cleavage ions with very little or no cross-ring fragments  (Figure 3.7a). Thus, they are of limited use for determining the detailed structure of unknown carbohydrates. Another problem is the tendency for rearrangement reactions to occur [284-288], particularly when the carbohydrate has been derivatized at the reducing terminus [289, 290]. Derivatization by reductive amination introduces a secondary amine at the reducing terminus that readily attracts a proton to give the [M+H]+ ion. Charge localization at this site produces a spectrum that contains mainly Y-type glycosidic fragments.