Fig. 5: Unexpected glycan fragments in the analysis of intact glycopeptides.

a The main pipeline for the analysis of Y ions in GPSMs. b Distribution of GPSMs containing specific pGlycoNovo-matched Y ions among co-identified GPSMs in each sample. c Annotated spectrum of a glycopeptide identified in mouse brain data (PXD025859²⁵) with low-energy HCD (HCD@20) fragmentation analysis. d Annotated spectrum of a glycopeptide identified in worm data with sceHCD (HCD@30 ± 10) fragmentation analysis. e Proportion of GPSMs containing specific Y ions in a particular glycan type. f Proportion of GPSMs containing specific pGlycoNovo-matched Y ions among co-identified GPSMs in the plant (left), and the proportion of GPSMs containing specific Y ions in a particular glycan type (right). g Annotated spectrum of a glycopeptide identified in plant data. In figure b, e, and f, blue font indicates Y-ions matched by both pGlycoNovo and pGlyco3, and fuchsias font indicates Y-ions exclusively matched by pGlycoNovo. In figure c, d, and g, spectra peaks are magnified for better visibility; unexpected fragment ions matched by pGlycoNovo are highlighted in red dashed boxes. The peptide sequence with “J” indicates the N-glycosylation site. the glycan symbols are as follows: green circle for Hex, blue square for HexNAc, red triangle for fucose, and yellow star for xylose.