Fig. 3

MRM analysis reveals quantitative differences in peptide presentation and suggests greater overlap in peptide repertoire. Relative abundance of peptide ligands bound to HLA-B*57:01 (blue triangles), HLA-B*57:03 (open purple diamonds) or HLA-B*58:01 (red circles) as detected by LC-MRM-MS. Peptides are categorised based on previous detection by LC-MS/MS as either binding a single HLA allotype (unique), two HLA allotypes (overlap) or all three HLA allotypes (common). On peptide detection the combined peak area for all MRM transitions, normalised against co-immunoprecipitated β₂m, was used to calculate relative abundance. Abundances are shown as a proportion of the maximum normalised peak area detected for the peptide across all experiments. Data are shown for three biological replicate experiments per allotype