Fig. 4

Protein expression of predicted neoepitopes in three rhabdomyosarcoma. For each of the three mutant peptides predicted to be antigenic, the corresponding tandem mass spectrometry (MS/MS) spectra are shown. During each round of MS/MS analysis, ions for the peptide being sequenced were fragmented into complementary ion pairs, with b- and y- ions corresponding to the N- and C-terminal fragments, respectively (as shown for each mutant peptide sequence, with the mutant amino acid highlighted in red). Peaks that match to theoretically calculated fragmented ions of the mutant peptide are indicated. The ions for the peptide itself (precursor ions) are indicated as (M + 2H)². a–c MS/MS spectra assigned to mutant peptides of xenograft samples derived from primary tumors of SJRHB011_E (a), SJRHB012_D (b), and relapsed tumor SJRHB026_S (c)