Table I. The sensitivity and false positive rate (FPR = 1-specificity) with the threefold decision criterion for Sample 6C (yeast + UPS1 at 2.2 fmol/μl) against Sample 6D (yeast + UPS1 at 6.7 fmol/μl) from the first lab in Study 6. Each of the runs from Sample 6C (run #7, 8, 9) was used in the numerator (base run) to calculate the relative intensities (M) in a pair with the runs from Sample 6D (run #10, 11, 12). The results in Column “before” used data before normalization. The results in Column “With A only” used data normalized by the abundance (A) only. The results in Column “With all variables” used data normalized by all variables. The normalization was based on common peptides selected using the global rank-invariant set in (18).

	Sensitivity			FPR
	Before	With A only	With all variables	Before	With A only	With all variables
Base run = 7	0.78	0.59	0.66	0.023	0.018	0.011
Base run = 8	0.31	0.56	0.78	0.016	0.018	0.011
Base run = 9	0.28	0.63	0.75	0.013	0.016	0.011