(a) Two RI neoepitopes identified in the MeWo cell line originating from gene KCNAB2 were both predicted in silico and found by mass spectrometry in the MeWo immunopeptidome. Integrative Genomics Viewer (IGV) sashimi plot indicating RNA-seq read depth (RI expression in TPM = 5.13, percent-spliced-in (PSI) value = 1.07%) and mass spectra. Experiments were repeated five times with independent measurements for cell line MeWo. Neoepitopes shown had one peptide-to-spectrum match (PSM) and were identified in one replicate within a 1% false discovery rate. CCLE, Cancer Cell Line Encyclopedia. (b) Predicted RI neoepitopes were found to have mass spectrometric evidence supporting their presentation in complex with MHC I using the same methodology in additional tumor cell lines: SK-MEL-5, CA46, DOHH-2, HL-60 and THP-1.
