The structural characterization of sulfated glycosaminoglycan (GAG) carbohydrates poses an analytical challenge due to a high level of heterogeneity inherent to a non-template based bio-synthesis and lability of the sulfate half-ester modification. Recently, tandem mass spectrometry has provided a sensitive method for the location of sites of sulfation in these complex biomolecules as well as determination of the stereochemistry of the C-5 carbon in hexuronic acid residues. In the presented work, electron-based ion activation methods, including electron detachment dissociation (EDD) and negative electron transfer dissociation (NETD), in conjunction with a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer have been applied to GAG glycoforms constituting all of the major sulfated classes (heparan sulfate, heparin, and chondroitin sulfates). In each case, the location of sites of sulfation are assigned and as well as hexuronic acid stereochemistry in cases where epimer pairs are available. In some epimer pairs, the application of chemometric analysis is required to distinguish the two diastereomers.