Scatter plots of FPR and TPR for unique peptides identified from three replicates for each algorithm using data set 2. (a) fraction 1, (b) fraction 2, (c) fraction 3, (d) fraction 4 and (e) fraction5. AB3D (filled circle), MZmine 2 (plus), MSight (filled diamond), SuperHirn (filled rectangle) and OpenMS (filled triangle). The same datasets (data set 2) were used to generate peak lists from those five algorithms. FPR for unique peptides are calculated using the average of each replicate FPR.