Efficiency of peak/protein predictions. We show boxplots summarizing the number of peaks predicted for each program in the mean spectrum of each dataset from HYBRID1 and HYBRID2 before thresholding. LibSELDI consistently predicts around 250 peaks, while MassSpecWavelet predicts more than 600 peaks consistently. MassSpecWavelet's more promiscuous predictions lead to high sensitivity at the expensive of higher false discovery rate performance. LibSELDI's peak predictions are reproducibly closer to the true number of virtual proteins, 150 of them, present in each dataset.