Table I. Sensitivity for accepting correct Peptide–Peptide Spectrum Matches: A set of simulated mixture spectra were constructed with mixture coefficients α = 1.0,0.5,0.3. Single-peptide probability, joint-probability and product probability were computed for the correct mixture matches as well as the top-scoring incorrect mixture matches returned by MixDB. Then each probability was used to separate correct from incorrect mixture matches. The false discovery rate is computed as the ratio of the number of accepted incorrect mixture matches over the total number accepted matches. The sensitivity of accepting correct matches at different FDR levels is shown.

Mixture coefficient	Probability	False discovery rate
		1%	2%	5%
α = 1.0	Single-peptide probability	71.9	74.7	81.8
	Joint probability	93.4	94.7	96.6
	Product probability	93.6	94.0	96.7
α = 0.5	Single-peptide probability	85.7	87.5	92.0
	Joint probability	93.5	94.3	96.0
	Product probability	92.6	94.1	96.1
α = 0.3	Single-peptide probability	89.4	90.8	92.8
	Joint probability	90.2	91.8	93.8
	Product probability	90.4	91.7	93.8