The most common approach to deduce the originating peptide behind an MS/MS spectrum is sequence database searching . It involves comparing MS/MS spectra against all theoretically possible peptides derived from the protein sequences present in the database, in combination with decoy sequences that are used for statistical confidence estimation . However, large databases, such as in immunopeptidomics, introduce challenges, such as an increase in random high-scoring matches, including high scoring decoys, resulting in fewer identifications at a given FDR (usually 1%) . Consequently, numerous informative spectra are discarded, leading to the oversight of many potentially therapeutically relevant targets.