The global COVID-19 pandemic has resulted in extensive efforts to develop vaccines for the novel coronavirus. Identifying vaccine targets relies on robust analytical methods to understand SARS-CoV-2 structural biology. This study focuses on reversed-phase liquid chromatographic analysis of the intact SARS-CoV-2 spike protein, which has emerged as a potential target for vaccine development due to its role in viral pathogenesis. This work demonstrates that using difluoroacetic acid (DFA) as a mobile phase modifier in place of formic acid (FA) results in increased chromatographic resolution during intact protein analysis. Furthermore, the results suggest that pairing this approach with N- and O-glycosidase treatments may enable more detailed intact protein MS investigations.