MS2 and MS3 Properties of Partially Deglycosylated Core Fucosylated Glycopeptides in Ion Trap

Large scale identification and quantification of core fucosylated glycoproteins are crucial for discovery and validation of fucosylation related cancer biomarkers. However, in glycoproteome research, mass spectra of glycopeptides are usually abandoned, because their tandem MS spectra are too complex to identify. In this research, we analyzed the MS 2 and MS 3 properties of partial deglycosylated core fucosylated glycopeptides in ion trap, which is much helpful for large scale and automatic identification of the core fucosylated glycoprotein. Several properties were illustrated. First, the retained intact GlcNAc residue frequently lost from the b and y ions, so these kinds of special product ions must be synchronously considered with GlcNAc attached b and y ions in searching. Second, losses sourcing from partial GlcNAc fragmentation were observed, which would often bring strong peaks. Third, diagnostic ions from GlcNAc residue were observed in MS 3 spectra in the low m/z range. Forth, Na + can instead of H + for ionization, but their intensities of fragment ions were much worse than parent ions only charged by H + . To void these interferers, these properties should be