Fig. 2.

(A) Example of MS/MS annotation of endogenous HLA-Ip identified as an LM_spliced peptide (DHAQQPYSM), (upper panel) MS/MS of the synthetic counterpart of the LM_spliced (lower panel). (B) MS/MS annotation of the same endogenous HLA-Ip as an alternative UniProt peptide (DHRSEQSSM, upper panel), and MS/MS of the synthetic counterpart of the alternative UniProt peptide (lower panel). (C) The cosine similarity score calculated for the 21 pairs of MS/MS spectra of LM_spliced peptides and their synthetic counterparts and the pairs of the alternative sequences from UniProt and their synthetic peptides.