Table 2.

False-positive and false-negative rates of peptide identifications in liver tissue predicted by PeptideProphet at different probability thresholds

Probability score cutoff	False-negative rate	False-positive rate
0.99	0.6042	0.0025
0.95	0.4037	0.0099
0.90	0.3297	0.0172
0.80	0.2621	0.0304
0.70	0.2252	0.0437
0.60	0.1964	0.0593
0.50	0.1713	0.0787
0.40	0.1440	0.1091
0.30	0.1262	0.1364
0.20	0.1041	0.1877
0.10	0.0724	0.3010
0.00	0.0000	0.9295