Fig. 2: Characterization of Benign_TOFIMS dataset.

a Sample overview included in the benign_TOFIMS dataset. b, c Population coverage of the HLA class I (b) and HLA class II (c) allotypes of the benign sample cohort compared to the world population determined by the IEDB population coverage tool⁴⁶. Frequencies of individuals within the world population carry up to 6/8 allotypes (x-axis) are indicated as bars on the left y-axis. The cumulative percentage of population coverage is depicted as dots on the right y-axis. d HLA class I (top) and HLA class II (bottom) ligand yields of the primary benign tissue samples of various origins (n = 94). Median peptide yields are indicated as lines and samples marked with asterisk were only characterized for HLA class II-presented peptides. e Tissue specific HLA class I and HLA class II peptide yields of the benign_TOFIMS dataset (n = 94 biologically independet samples). Mean peptide yields ± standard deviation are depicted with error bars. f Percentage of peptides included in one, two or three technical replicates within one sample in the benign dataset (n = 94 biologically independet samples). Mean peptide overlap ± standard deviation are depicted with error bars. g HLA class I and HLA class II peptide length distribution of the benign dataset. h, i HLA class I (h) and class II (i) peptide overlap of tissues originating from the same donor (n = 16 for UDN01, n = 12 for UDN02, n = 20 for UDN04 and n = 11 for UDN08) with corresponding chord plot analysis. AG Adrenal gland, BM Bone marrow, SI Small intestine, LN Lymph node, esoph. esophagus, UDN Universal donor number, HLA Human leukocyte antigen, cumul. Cumulative, pop. Population, cov Coverage. Source data are provided as a Source Data file.