Table 5. Performance of the target alternative k-permuted decoy databases used with the OMSSA database search program using spectra from 80 unmodified neuropeptides.

Databasea	Indicatorb	Significance Levels of the Permutation p-values c							Cum. Num. of Peptidesd
		0	1	2	3	4	5	≥6	≥10−2	≥10−4
Target	E-value	0	0	1	2	1	3	73	80	77
K103	# ions	0	2	78	0	0	0	0	78	0
	Lambda	0	9	71	0	0	0	0	71	0
	p-value	0	2	78	0	0	0	0	78	0
	E-value	0	2	78	0	0	0	0	78	0
K104	# ions	0	0	1	79	0	0	0	80	0
	Lambda	0	5	11	64	0	0	0	75	0
	p-value	0	0	1	79	0	0	0	80	0
	E-value	0	0	1	79	0	0	0	80	0
K105	# ions	0	0	0	0	80	0	0	80	80
	Lambda	0	5	8	24	43	0	0	75	43
	p-value	0	0	0	0	80	0	0	80	80
	E-value	0	0	0	0	80	0	0	80	80
K106	# ions	0	0	0	0	2	78	0	80	80
	Lambda	0	5	8	17	18	32	0	75	50
	p-value	0	0	0	0	0	80	0	80	80
	E-value	0	0	0	0	0	80	0	80	80

^aTarget: database of 236 neuropeptide sequences; K10³: k-permuted decoy database size of 236,000 peptides; K10⁴: k-permuted decoy database size = 2,360,000 peptides; K10⁵: k-permuted decoy database size = 23,600,000 peptides; K10⁶: k-permuted decoy database size = 236,000,000 peptides.

^b# ions: permutation p-values computed for the number of matched b- and y-ions. Lambda: permutation p-values computed from the Poisson mean of matches. p-value: permutation p-values computed from the p-value reported by the OMSSA for the matches. E-value: permutation p-values computed using OMSSA E-values.

^cSignificance threshold (t) for matched to be considered significant at p-value<1×10^−t.

^dIncorrect: the program provided an incorrect match.

^eCumulative number of peptides with p-value<1×10⁻².

^fCumulative number of peptides with p-value<1×10⁻⁴.