Extended Data Fig. 9: Examination of biased-anchor peptide ligands.

(a) Schematic representation of the library design used to examine biased-anchor peptide ligands. The favored residues at each anchor position are shown for the indicated MHC-I allele; peptides selected for characterization by EpiScan contained a favored residue at one of the critical anchor positions but an unfavored residue at the other. (b) Evaluation of biased-anchor binders by EpiScan. The percent of binders for the given fixed residues at each anchor position are shown. (c) Logoplots summarize the sequences of the MHC-I ligands identified by EpiScan for HLA-A*02:01 where the ninth position has been fixed with either leucine or valine and isoleucine, leucine, methionine and valine are excluded from the second position. (d) Statistical analysis of the residues at the fourth position of biased-anchor HLA-A*02:01 ligands identified by EpiScan that ended with either L or V. A positive percent difference indicates a larger fraction of that amino acid occurred in L-ended peptides relative to V-ended peptides. P-values were determined by a two-tailed Fisher’s exact test, comparing amino acids at the fourth position across the two conditions (only those seen at least seven times are shown). (e to h) Logoplots summarizing the composition of biased-anchor MHC-I ligands identified by EpiScan, wherein one anchor position contains a favored residue but the other anchor position does not: (c) HLA-A*02:01, with positions 2 and 9 as anchors, (d) HLA-A*03:01, with positions 2 and 9 as anchors, (e) HLA-B*08:01, with positions 5 and 9 as anchors, and (f) HLA-B*57:01, with positions 2 and 9 as anchors.