Extended Data Figure 1. Identification of N-glycopeptides and N-glycans.

(a) Glycopeptide MS/MS raw-data were pre-processed and identified using different MS/MS search engines: Mascot (orange), SEQUEST-HT (blue) and X!tandem (green). The glycopeptide sequences identified by these algorithms were highly similar, both with respect to identities and numbers. (b) The N-glycosylation sites identified in our study (orange) were mapped to published annotated N-glycosylation sites in Uniprot (grey) and those identified by Wollscheid et al.⁷ (green). (c) Negative-mode MALDI-TOF analysis of 2-AA labelled N-glycans from mESCs directly correlated with the N-glycan profiles identified using our glycoproteomics approach.