MS data were searched with Byonic (v4.3.4) using a list of common mammalian O-glycans to verify O-glycan composition on glycopeptides. Scheme S1 shows a set of the symbols used for common saccharides and representative glycan linkages. Two glycan modifications were allowed per peptide and up to 6 missed cleavages were allowed. Variable modifications included the oxidation of methionine (+15.99 Da) and deamidation of asparagine and glutamine (+0.98 Da). Precursors were allowed a 10-ppm error tolerance while fragment ions were retained if they fell within a 20-ppm mass tolerance. A 1% FDR was used for every search. Identified glycopeptides by HCD, EThcD, and UVPD were considered valid at a PEP 2D score less than 0.01 and a Byonic score above 300. Glycopeptides identified in Byonic were subject to manual validation using GlycoWorkbench (v1.2.4105), as detailed previously. Core saccharide linkages (e.g. Galβ1-3GalNAc) were not evaluated in this study. Venn diagrams were generated using Venny 2.1.