Immunopeptidome overlaps of HLA-DP allotypes from different TCE groups and their dependency on HLA-DM. (A) Percentage of unique peptides shared between the HLA-DP immunopeptidomes from BLCLs expressing the indicated paired allotypes, characterized as described in van Balen et al.8 Data from at least 2 biological and 3 technical replicates were coprocessed for the analysis. Blue- and red-lined boxes represent permissive and nonpermissive allotype combinations with a mean ± standard deviation (SD) overlap percentage of 24.0 ± 16.5 and 2.0 ± 1.3, respectively (P < .001 in 2-tailed unpaired t test). Peptide repertoire overlaps between ≤3 different BLCLs expressing the same HLA-DPB1 allele were determined for HLA-DPB1*02:01, 03:01, and 04:01 and had a mean of 41.4% ± 8.1%. (B) Peptide overlap in permissive (DP401 vs DP402) or nonpermissive (DP401 vs DP10) HLA-DP allotype combinations determined in the same cellular background of transduced HeLa cells in the presence of HLA-DM. Numbers indicate unique or shared peptides, the latter with its percentage relative to the combined data set. Data from at least 2 biological and 3 technical replicates were coprocessed for the analysis. (C) Overlap between peptides retrieved from DP402 or DP10 expressed by HeLa cells in the presence or absence of HLA-DM. Numbers indicate unique or shared peptides and the percentage of numerical inflation of the peptide repertoire in the absence of HLA-DM relative to its presence. (D) Volcano plots showing unique peptides significantly enriched in the presence (green) or absence (red) of HLA-DM for DP402 and DP10. Significant enrichment was assigned to peptides with at least twofold variation of relative abundance in the presence vs absence of HLA-DM and significant (P < .01) in false discovery rate–adjusted 1-way analysis of variance (ANOVA).