Table 6.

The percentage of the total number of peptides identified, allowing multiple co-eluted peptides per spectrum, when compared to that of the single peptide identification at a fixed E-value.

	CTP2/CTP1		CTP3/CTP1
	E = 10-2	E = 10-1	E = 10-2	E = 10-1
RAId_DbS (U)	1.22(1.21)	1.40(1.31)	1.26(1.26)	1.53(1.55)
X!Tandem (U)	1.24(1.22)	1.34(1.31)	1.27(1.25)	1.44(1.41)
Mascot (U)	0.95(0.83)	1.15(1.05)	0.87 (0.64)	1.13(1.13)
SEQUEST (U)	0.95(1.10)	1.10(1.12)	0.92(1.01)	1.11(1.22)
OMSSA (U)	1.05(1.06)	1.02(1.06)	1.11(1.01)	1.08(1.12)

To the right of each search method, the first number in each grid is the ratio of number of identified peptides using the compound spectra to that using single peptide spectra at various E-value cutoff. The number in parentheses is the ratio obtained by using only compound spectra constructed from mixing the spectra of unique peptides. Here the symbol "U" stands for "unique peptide". The symbols CTP1, CTP2 and CTP3 correspond respectively to the cumulative number of true positives (TP) identified with E-value equal to or smaller than the specified cutoff when analyzing single-peptide spectra, compound spectra of two peptides, and compound spectra of three peptides.