Table 2. Variability in PSM Discoveries Reported by Different Applications of TDC Using Calibrated and Raw XCorr Scores.

		% only in one T-TDC raw score			% only in one T-TDC calibrated score
set	FDR	0.01	0.05	0.10	0.01	0.05	0.10
yeast	0.05 quantile	0.1	0.5	1.1	0.0	0.1	0.3
	median	1.0	0.9	1.6	0.6	0.6	0.8
	0.95 quantile	3.1	2.1	2.8	2.4	1.7	2.0
worm	0.05 quantile	0.1	0.6	1.5	0.0	0.2	0.5
	median	1.5	1.5	2.5	1.1	0.8	1.2
	0.95 quantile	4.7	3.5	4.6	3.9	2.5	3.0
Plasmodium	0.05 quantile	0.0	0.6	1.4	0.0	0.1	0.2
	median	1.1	1.3	2.2	0.6	0.5	0.7
	0.95 quantile	6.0	3.3	3.9	2.6	1.6	2.3