Fig. 4: Semi-supervised deconvolution of glycosylated HLA peptides from Ramarathinam et al.³⁶ using MoDec.

Panels I show the percentage of peptides and glycopeptides presenting the HLA-binding motif. Panels II display the glycosylation absolute position within the peptidic sequence (x-axis) and the peptide length (y-axis). Gray and black lines indicate the N-term and C-term, respectively, whereas the white to blue gradient represents the number of peptides with a specific glycosylation position at a specific peptide length. Panels III present the HLA-binding motif after deconvolution with MODEC (top) and the number of glycopeptides per relative glycosylation position (bottom). Negative values refer to glycosylation positions upstream of the HLA-binding core; values between 0 and 8 represent positions within the HLA-binding core; and values ≥ 9 refer to positions downstream of the HLA-binding core. Panel I includes both regular and glyco-search peptides, whereas Panels II and III show only glycopeptides from the union of all replicates per allele. a Peptides associated with the HLA allele DPA1*02:01/02-DPB1*04:01 of the C1R cell line. b Peptides associated with the HLA allele DQA1*05:05-DQB1*03:01 of the C1R cell line. c Peptides associated with the HLA allele DRB1*12:01 of the C1R cell line. d Peptides associated with the HLA allele DRB3*02:02 of the C1R cell line.