Comparative HLA class I ligandome profiling and identification of CML-associated antigens. (A) Saturation analysis of HLA class I ligand source proteins of the CML patient cohort. Number of unique HLA ligand source protein identifications are shown as a function of cumulative HLA ligandome analysis of CML samples (n = 21). Exponential regression allowed for the robust calculation (R² = 0.9999) of the maximum attainable number of different source protein identifications (dotted line). The dashed red line depicts the source proteome coverage achieved in our CML patient cohort. (B) Overlap analysis of HLA class I ligand identifications of primary CML samples (n = 21), CML_MR samples (n = 15), and hematological benign samples (n = 108), including PBMCs (n = 63), granulocytes (n = 14), CD19⁺ B cells (n = 5), bone marrow (n = 18), and CD34⁺ HPCs (n = 8). (C) Comparative profiling of HLA class I ligands based on the frequency of HLA-restricted presentation in CML and hematological benign ligandomes. Frequencies of positive immunopeptidomes for the respective HLA ligands (x-axis) are indicated on the y-axis. To allow for better readability, HLA ligands identified on <5% of the samples within the respective cohort were not depicted in this plot. The box on the left and its magnification highlight the subset of CML-associated antigens showing CML-exclusive high frequent presentation. Allotype-specific comparative profiling of HLA-A*02–positive (D), HLA-A*03–positive (E), HLA-A*11–positive (F), and HLA-B*07–positive (G) samples, as described above. ID, identifications; pos., positive.