Conformation of glycosaminoglycans by ion mobility mass spectrometry and molecular modelling

We have performed conformational analyses of heparin-derived oligosaccharide ions in the gas phase using a combination of ion-mobility mass spectrometry and molecular modelling. Negative mode electrospray ionisation was used to generate singly (disaccharide, [C 12H 15NO 19S 3Na 3] -) and doubly charged (tetrasaccharides, [C 24H 30N 2O 38S 6Na 6] 2- and [C 24H 31N 2O 35S 5Na 5] 2-) ions containing three and six Na + ions, respectively. Good agreement was obtained between the experimental and theoretical cross sections. The latter were obtained using modelled structures generated by the AMBER-based force field. Analysis of the conformations of the oligosaccharide ions shows that sodium cations play a major role in stabilizing these ions in the gas phase. This was seen in the formation of oligomers of the disaccharide ion and "compact" structures of tetrasaccharide ions. Interestingly, the gas phase conformations of the three tetrasaccharide ions with different primary structures were significantly different. © The Owner Societies 2005.