Fig. 3.

PREGO Scores for peptides in CASZ1. Peptides in CASZ1 (also known as cDNA FLJ20321) are ranked on their experimentally acquired transition fragment intensity from the Stergachis et al. SRM testing data set where the peptide with the strongest response is awarded a rank of one. The top 20% of peptides by intensity rank are considered “high-responding peptides” and are shaded in blue. The top five peptides chosen by PREGO are marked with red borders. Although there is large variation in predicting response intensities for any given peptide (solid line), there is a definite trend (dashed line) to score first ranked peptides somewhat higher than worse ranked peptides. Consequently, the highest scoring peptides picked by PREGO are often also high-responding peptides. CASZ1 represents a “typical” protein with a correlation score of 0.65.