Glycosaminoglycans use positional sulfation to encode binding specificity onto its sequence. Understanding these sulfation patterns constitute a major challenge. Previous studies hinted that sulfate groups can migrate along glycans during collision-induced dissociation in mass spectrometry (MS) experiments, forming isomeric fragments that can lead to incorrect structural assignments. We use ion-mobility – mass spectrometry to investigate the mechanism of this phenomenon in heparin sulfate disaccharides. The sulfate group migrates from the non-reducing to reducing end of the sugar, and the degree of migration does not depend on the structure of the label. The migration product has a sulfate group attached to either 6O- or 3O-position of GlcNAc, and the migration mechanism consists of multiple steps, with the sulfate group first shifting from the iduronic acid to the 6O-position of GlcNAc, and next to the 3O-position. The presented data offer insight into the complexity and unpredictability of sulfated sugar fragmentation in tandem MS and extensive investigations is required to determine whether this represents a singular case or a general phenomenon characteristic of deprotonated sulfated glycans.