Figure 5.

The PeptideProphet fit to the Human Plasma dataset of Tandem scores of Charge 2. The PeptideProphet fit to the Human Plasma dataset of Tandem scores of Charge 2 with fitted frequency curves from Figure 2b. The four confidence measures of the Posterior Error Probability (PEP), p-value, False Discovery Rate (FDR), and False Positive Rate (FPR) are shown at a score of 1. The Posterior Error Probability at 1 is 0.156 and the estimated False Discovery Rate is 0.083. The p-value and FPR are equivalent and equal to 0.004. In the formula for the estimated FDR, red is the estimate for V from Table 1 while blue combined with red is an estimate for R from Table 1.