Fig. 5: Fully unsupervised deconvolution of glycosylated HLA peptides from Ramarathinam et al.³⁶ using NetMHCIIpan 4.1.

Each panel illustrates two levels of information: the top level shows the HLA-binding motif of peptides passing a NetMHCIIpan 4.1 percentile rank threshold of 20 after binding affinity prediction. The bottom level shows glycopeptides that are predicted to bind to a given allele in green (%rank ≤ 20); otherwise, non-binding peptides (i.e., trash) are shown in red (%rank > 20). Positions are shown relative to the HLA-binding core with negative values referring to the glycosylation position 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. a Deconvolution of glycosylated peptides associated with the HLA-DPA1*02:01/02-DPB1*04:01 alleles. b Deconvolution of glycosylated peptides associated with the HLA-DQA1*05:05-DQB1*03:01 alleles. c Deconvolution of glycosylated peptides associated with the HLA-DRB1*12:01 allele. d Deconvolution of glycosylated peptides associated with the HLA-DRB3*02:02 allele.