Another potential drawback to using database search results to evaluate de novo methods is that the resulting performance estimates are unrealistically good. In practice, typically only around 25-50% of the given spectra in a dataset can be confidently identified using database search procedures . A priori, we expect these identified spectra to have a greater proportion of diagnostic b-and y-ion peaks and an overall lower noise level than the unidentified spectra. Hence, when a de novo sequencing paper reports that a method correctly identifies, say, 60% of the spectra, this number typically represents the correct identification of only ∼30% of the full dataset. The rate of correct identifications that the method can achieve on the remaining 50% of the data is almost certainly much lower than 60%.