(a) Venn diagram showing the overlap between high-confidence H2Db/Kb-associated peptides identified from 19 healthy tissues and 4 tumor cell lines used in this study. (b) Cumulative number of MS/MS spectra acquired versus cumulative number of distinct high-confidence H2Db/Kb peptides identified. Each data point represents an added injection/MS experiment, and the experiments are presented in a chronological order of data acquisition (see Order of injection for H2Kb peptides; Data Citation 1 and Order of injection for H2Db peptides; Data Citation 1). (c) Histogram indicating the number of distinct peptide ions that were generated from normal tissues using different fragmentation methods (i.e. Orbitrap CID, HCD and CID-QTOF). High-quality MHC allele- and fragmentation-specific peptide spectral libraries were generated using SpectraST. (d) Venn diagram showing the overlap between high-confidence H2Db/Kb-associated peptides generated from normal tissues using different fragmentation methods. (e) Screenshot of SysteMHC Atlas (https://systemhcatlas.org/). The raw MS output files, the peptide sequences and the spectral libraries are accessible at SysteMHC Atlas with the dataset identifier SYSMHC00018.