Figure 3.

Comparison of score distributions of all peptides identified in the search versus peptides containing SAPs. For Jurkat cells, the distribution of SEQUEST XCorr Scores for peptides passing a 1% false discovery rate were compared between 1) peptides mapping to the Ensembl reference proteome, and 2) peptides containing single amino acid polymorphisms (SAPs) derived from the sample-matched RNA-Seq data. SAP-containing peptides had, on average, higher peptide spectral match (PSM) quality scores as compared to those of reference peptides, attesting to the high quality of the sample-specific SAP database employed for MS searching.