Fig. 4: Sensitivity and specificity of MHCvalidator.

a Histogram illustrating the number of HLA-I-specific peptides that were deemed of high-confidence by MHCvalidator and Percolator (y-axis) following twofold serial dilutions of HLA-I peptides isolated from JY cells (x-axis). Fold-increase of peptides identified by MHCvalidator over that of Percolator is indicated for each dilution. The benchmarking reference used for comparisons corresponds to the peptides that were identified by Percolator in the undiluted sample (–). Legend: Peptides identified by Percolator (blue) and MHCvalidator (red) found in the benchmarking reference; high-confidence peptides not found in the benchmarking reference by Percolator (pale blue) and MHCvalidator (pale red). Distribution of XCorr values (b) and peptide length (c) for PSMs found uniquely with MHCvalidator versus those found with Percolator from the most diluted JY sample (16x). We performed a standard independent 2-sample t-test that assumes equal population variances for these instances. Box plot showing the number of HLA-I-specific PSMs “deemed high-confidence” that were found in a yeast proteome (d) or human proteome digested with Lys-C (e) using Percolator and the four configurations of MHCvalidator (NN-validator only, NN-validator and PE, NN-validator and APP, as well as NN-validator with PE and APP). Boxplots/error bars are based on 1550 samples derived from the monoallelic dataset (d). The LysC digestion analysis is based on a subset of these data, 145 samples in total that were randomly selected from the complete monoallelic dataset (e). Boxplots are given in Inter Quartile Ranges (IQRs) where the box extends from the first quartile (Q1) to the third quartile (Q3) of the data, with a line at the median. The whiskers extend from the box to the farthest data point lying within 1.5x the inter-quartile range (IQR) from the box. Flier points are those past the end of the whiskers. Source data are provided as a Source Data file.