Fig. 4. Functional immunopeptidomic validation.

a Functional immunopeptidomic validation was performed using paired tumor and adjacent normal fresh frozen samples. HLA-B2M complexes were purified from each sample and peptides were gently eluted. Peptides from each sample were labeled with TMT tags and measured using quantitative mass spectrometry. b Box plots showing the log2 fold change of peptide intensity between lost, kept, and homozygous alleles across all six patients. HLA-A is represented by 1490 peptides in the ‘lost’ category, 6613 peptides in the ‘kept’ category, and 2814 peptides in the ‘homozygous’ category. HLA-B is represented by 3823 peptides in the ‘lost’ category and 9910 peptides in the ‘kept’ category. HLA-C is represented by 703 peptides in the ‘lost’ category, 3421 peptides in the ‘kept’ category and 620 peptides in the ‘homozygous’ category. The center of the box denotes the median value, the box denotes the quartiles and the whiskers denote the remainder of the distribution apart from outliers. Statistical significance was assessed using a two-sided student T-test with asterisks denoting p-values < 0.05. Source data are provided with this paper.