The sensitivity and specificity limitations make it challenging to confirm neo-epitopes in short non-tryptic peptide sequences. A recent study analyzed ca. 170,000 synthetic peptides using LC-MS/MS and found that over 10% of the assigned spectra did not correspond to the respective references when analyzed using standard methods, highlighting the significance of using dependable reference peptides, such as NeoSpikeMix, in immunopeptidomics.
