Establishing MHC class I peptide motifs

Major histocompatibility complex (MHC) class I peptide motifs are used on a regular basis to identify and predict MHC class I ligands and CD8(+) T-cell epitopes. This approach is above all an invaluable tool for the identification of disease-associated epitopes. As a matter of fact, the vast majority of T-cell epitopes discovered during the past two decades was identified by means of epitope prediction. Here we describe the steps which are necessary to establish MHC class I peptide motifs and to compose a reliable scoring matrix for epitope prediction. As an example, a scoring matrix for the prediction of HLA-B*35-presented T-cell epitopes will be developed by examining the characteristics of 76 naturally presented HLA ligands.