Assessing the reliability of binding prediction methods for the identification of naturally processed MHC-epitopes.

(a) Box plots showing the quartile distribution of binding affinity rankings as predicted by NetMHC4 and NetMHCpan4 for MHC-eluted and non-eluted peptides. Grey dashed line indicates predicted binder ranking of top 2%. (b) FDr and FNr values calculated based on top 2% percentile rank cutoff on three MS-derived datasets visualized as heatmap. Similar plots of predicted scores are shown in S4 Fig.