Recognition of Core-Fucosylated Glycopeptides Based on the Y1+Fuc/Y1 Ratio in Low-Energy HCD Spectra

Accurate identification of core fucosylation on N-glycopeptides remains challenging due to fucose migration
during
mass spectrometry analysis. Here, we introduce a simple and straightforward
method for core-fucosylated glycopeptide recognition based on the
relative intensities of Y1+Fuc ions compared with their corresponding
Y1 ions (labeled as Y1+Fuc/Y1 or simply Y1F/Y1 ratio > 0.1) in
low-energy
HCD-based spectra. The method was first developed by systematically
evaluating the influence of fucose migration on the Y1F ion from antenna
fucoses based on the distribution of the Y1F/Y1 ratios in the MS/MS
spectra of antenna-fucosylated glycopeptides from Fut8–/– mouse brain. The feasibility of the method was then confirmed by
using two standard glycoproteins, comparison with glycopeptides in
Fut8+/+ mouse brain with/without in silico core-fucosylation
removal, and Y1F/Y1 ratio alterations under a lower HCD energy. This
method will be applicable to the manual interpretation and software-based
high-throughput analysis of core-fucosylated glycopeptides.