Table 1. Glycopeptides identified using two different search approaches. Conventional: all oxonium ions spectra were searched for glycopeptides.

		Assigned MS/MS spectra	Unique glycopeptides	Peptide backbones	Glycan compositions	Accuracy of classification
N-glycopeptides	Conventional	1065	403	98	63	99.7%
	Pre-classification	1481	529	123	80	100%
O-glycopeptides	Conventional	200	32	4	31	96%
	Pre-classification	193	32	4	31	100%

Pre-classification: oxonium ions spectra were separated by classification model and searched for respective N- and O-glycopeptides. The results show that pre-classification of the oxonium ion containing spectra improves the identification of N-glycopeptides, however it does not impact the identification of O-glycopeptides.