In this application note, we demonstrate that UPLC/MSE is capable of separating and characterizing N-linked glycosylations of hemagglutinin (HA) proteins in a recombinant influenza vaccine candidate expressed from insect cell-baculovirus expression vector system (BEVS). Glycopeptides and glycoforms are separated by an ACQUITY UPLC System at the peptide level, and are detected online by a SYNAPT MS System. The UPLC/MSE data are processed by BiopharmaLynx Software to report N-linked glycosylation information. The method offers a way to improve the characterization as well as reduce the amount of time spent on data processing. Furthermore, having a general technique that can be applied to such problems opens this type of analysis to non-experts and could benefit an organization by streamlining their work.