Figure 2.

Simulation of ungrouped, grouped, and cascade FDR procedures. (A) Plots, for each procedure, of the number of identified spectra as a function of FDR threshold. (B) Plots, for each of the three groups, of the actual FDR produced by each of the three procedures. (C) Proportion π₀ of PSMs that are marked false for each group. (D, E) Same as panels A and B but for a simulation in which the FDR estimates include the actual value of π₀. All simulations were repeated 100 times; means and standard deviations are indicated.