An additional complication in evaluating de novo sequencing is the presence of chimeric spectra, i.e., those generated by two or more peptides that co-fragment in the mass spectrometer. Even for current evaluation schemes, a chimeric spectrum generated by two peptides may be assigned the first peptide by the database search procedure and the other peptide by the de novo sequencing algorithm. This correct identification would be deemed incorrect according to the gold standard. Predicting chimeras in a de novo manner is challenging, and evaluating such predictions is even more complex.