The peptide identification sensitivity of the affinity purified immunopeptidome of a JY cell line (Epstein–Barr virus-immortalized B cell lymphoblastoid line, ECACC 94022533, IHW9287) for DDA and DIA experiments was assessed by a linear concentration series. JY cells are homozygous for all HLA-I loci (HLA-A*02:01, HLA-B*07:02, and HLA-C*07:02). The JY HLA-I ligandome was isolated through immunoaffinity purification, as described in Marcu, Bichmann and Kuchenbecker et al 2021.