High Performance Anion Exchange Chromatography (HPAE) has long been used to separate ions and polar molecules. Here, we demonstrate that HPAE can be coupled to an Orbitrap™ mass spectrometer (IC-MS) to facilitate the separation and sequencing of sulfated O-glycan alditols. Porcine gastric mucin (type III) harbors high levels of sulfated but fewer sialylated glycans, and after release and rapid purification, these O-linked glycans were directly injected and analyzed. However, to analyze bovine submaxillary mucin, which harbors fewer sulfated but more sialylated O-glycans, a new workflow based on weak anion exchange (WAX) fractionation was necessary to minimize ion-suppression by the sialylated glycans. Using a post column splitter, 60% of the flow was desalted with an electrochemically regenerated desalter prior to introduction into the mass spectrometer. Due to the ability of HPAE to resolve isomers, 27 sulfated O-linked glycans were identified from Porcine gastric mucin (type III), and 9 from bovine submaxillary mucin. Using the data-dependent mode of the Thermo Scientific™ Q Exactive™ hybrid quadrupole-Orbitrap mass spectrometer, highly informative MS2 spectra enabled confident identification of the separated species.