Structural assignment of permethylated oligosaccharide subunits using sequential tandem mass spectrometry

The sequential tandem mass spectrometry (MSn) capabilities offered by quadr upole ion trap instruments have been explored in a systematic study of perm ethylated oligosaccharides, Under collision-induced dissociation, protonate d molecular species generated in the electrospray ionization mode yield sim ple and predictable mass spectra, Information on sequence, branching, and, to some extent, interglycosidic linkages can be deduced from fragments resu lting from the cleavage of glycosidic bonds. Simple rules for the structura l assignment of carbohydrates have been established for the fragmentation o f protonated species and submits thereof and corroborated by O-18-labeling experiments. Moreover, sequential tandem mass spectrometry was demonstrated to allow the straightforward structural characterization of unknown carboh ydrate moieties by comparing their CID spectra with those of a set of refer ences. As the collision-induced dissociation patterns are not dependent on the number of prior tandem mass spectrometric steps, structures can be unam biguously assigned by match of the spectra. These findings establish the ba sis of MSn performed on a quadrupole ion trap instrument for elucidating st ructures of large carbohydrates, which can be virtually degraded in the mas s spectrometer into smaller entities in one or several steps. This powerful technique has been applied, used in conjunction with specific CD3 labeling , to the characterization of series of subunits generated from fucosylated and sialylated oligosaccharides, which are among the most important structu res as far as biological activities are concerned.