Figure 4.

The protein absence ratio can be estimated by the classical decoy–target ratio, as long as we compensate for the absent protein fraction ${\pi }_A$. We plotted the reported fraction of absent proteins as a function of the classical decoy–target ratio (red), together with a line $y=x$ (solid, black) and $y={\pi }_A·x$ (dashed, blue) for ten randomized simulations with 20 000 peptide inferences. The protein absence ratio roughly corresponds to the classical decoy–target ratio times the absent protein fraction.