(a) 19 different tissues from C57BL/6 mice were extracted (Table 1) (Annotation Table, Data Citation 1). H2Db and H2Kb-associated peptides were isolated independently by immunoaffinity purification using the monoclonal antibodies B22-249.R1 and Y-3, respectively. Eluted peptides were identified by different LC-MS/MS systems in DDA mode. (b) MS output files were converted, searched, and statistically validated using the indicated software tools. The identified peptides were then clustered (GibbsCluster v.1) and annotated by length and predicted MHC binding affinity (NetMHC v.4). The final list of high-confidence MHC-associated peptides were used to build high-quality H2Db- and H2Kb-specific peptide spectral and assay libraries, which were deposited and shared via SysteMHC Atlas and SWATH Atlas, respectively.