Fig. 3. Validation of novel peptide identifications.

a PepQuery2 classified previously reported PSMs supporting novel peptides resulted from W to F substitution into seven categories as described in Fig. 1, and only C7 PSMs passed the validation. b PeptideProphet probability distributions for different categories of the PSMs. c The percentages of PSMs (C4) from W2F peptides in which the spectrum matched equally or better to a reference peptide with or without containing amino acid W. d The spectrum originally matched to a W2F peptide has better match to a reference peptide containing amino acid W in PepQuery2 validation. e Delta RT distributions for PSMs passing or failing PepQuery2 validation. The p-value was calculated using two-sided Wilcoxon rank sum test. For boxplots, centerline indicates the median, box limits indicate upper and lower quartiles, whiskers indicate the 1.5 interquartile range. Source data of 3a, 3b, 3c and 3e are provided as a Source Data file.