HLA-I binding affinity of peptide length variants located in the CLIP region of the invariant chain.

*Peptide found with HLA-I elutions.†Amino acid (AA) position in the invariant chain protein.‡Predicted HLA-I allele to which the peptide binds. Peptide binding prediction was done with netMHC (http://www.cbs.dtu.dk/services/NetMHC). Binding predictions can be made for peptide lengths between 8 and 11 for all alleles with a novel approximation algorithm using artificial neural networks trained on 9-mer peptides [26], [27]. Only peptides are shown with a predicted binding affinity of 500 nM or stronger.§IC50 is the concentration used to obtain half maximal competition and represents the mean value of two independent experiments.¶Binding affinity is classified according to the following IC50 cut-off values: high affinity, ≤5 µM; intermediate (int) affinity, 5–15 µM; low affinity, 15–100 µM; no binding, >100 µM [21].