Figure 1. Intensity of glycan oxonium ions differs between HCD fragmented O- and N-glycopeptides.

The MS/MS spectra of HCD fragmented glycopeptides with (A) O- and (D) N-glycans are shown. Focusing on the lower mass range that covers the oxonium ions for (B) O- and (E) N-glycans shows that these two glycosylation types create very different patterns of fragment ions in this range for the N-linked N3H3F0S1 (C) and O-linked N4H5F0S1 (F) glycan structures. The illustrated glycans depict possible structures for each glycan composition. There are several differences in the intensities of the oxonium ion between these two glycopeptides. Among these differences are the intensity ratios of HexNAc oxonium ions at 138, 168, 186 and 204, the intensities of Neu5Ac oxonium ions at 274 and 292 and the intensity of HexHexNAc oxonium ion at 366. Glycoworkbench³⁵ was used for creating the glycan structure figures. Blue square: GlcNAc; yellow square: GalNAc; white square: HexNAc; yellow circle: Galatose; green circle: mannose; white circle: Hexose; purple diamond: N-Acetylneuraminic acid (Neu5Ac).