Scatter plots of FPR and TPR for unique known peptides identified from four replicates for each algorithm. Standard peptide mixture with BSA concentration (a) 96 amol, (b) 480 amol, (c) 2400 amol, (d) 12 fmol, (e) 60 fmol and (f) 300 fmol. AB3D (filled circle ), MZmine 2 (plus), MSight (filled diamond), SuperHirn (filled rectangle), and OpenMS (filled triangle). The same datasets (data set 1) were used to generate peak lists from those five algorithms. FPR for unique known peptides are calculated using the average of each replicate FPR.