Given the array of large glycans, MUC-16 was explored for deeper analysis of the glycoforms, including site-by-site analysis of glycans with contributions to the overall glycopeptide mass of 859 Da or more (representing glycans containing four or more saccharides). Not only was each glycosite analyzed for different structural patterns of the same glycan composition but also the linkages of identical glycan compositions were dissected. The characterization of large O-glycans is notoriously difficult as there are several combinations of glycan-specific ions that correspond to the same m/z value, such as cross-ring cleavages associated with localizing Neu5Ac linkages to Gal, resulting in 1,3 A2 and 0,4 A2 ions, each having m/z values of 352.12). To illustrate the importance of cross-ring cleavages, Figure the various combinations of branching and linkage patterns that can arise, some of which are illustrated in Table . The fragmentation pattern generated by UVPD provides sufficient information to elucidate the exact structure of the glycan, thus disambiguating the branching pattern and linkage positions. The fragmentation pattern from EThcD (Figure ) is sparser and lacks sufficient fragment ions to deduce linkages between the saccharides. UVPD unlocks the potential for in-depth O-glycoproteomics analysis; however, even more sophisticated software tools are needed to streamline data analysis for higher throughput workflows. The current data analysis strategy requires rigorous manual validation for UVPD data.