Presentation of lymphoma immunoglobulin peptides by MHC. FL/DLBCL (A) and CLL (B) specimens were lysed, and MHC-I and MHC-II were immunoprecipitated in parallel. MHC-bound peptides were acid-eluted, fractionated by LC, and analyzed by MS. MHC-I (gray) and MHC-II (blue) bound peptides are depicted. Somatically mutated residues (either through somatic hypermutation or VDJ rearrangement) are shown in red. (C) Heatmap depicting the number of total class I (top) and class II (bottom) ligands across the immunoglobulin heavy chain for all patients. Both germline-derived and neoantigen peptides are included. The bar plots represent the number of neoantigen peptides spanning each position of the heavy chain for class I (top) and class II (bottom). CDR, complementarity-determining region; FR, framework region; IGHV, immunoglobulin heavy-chain variable region; IGLV, immunoglobulin light-chain variable region.