Table 3. Performance of the target and alternative k-permuted decoy databases used with the X! Tandem database search program using spectra from 80 unmodified neuropeptides.

Databasea	Indicator	Significance Levels of the Permutation p-values b							Cum. Num. of Peptidesc
		0	1	2	3	4	5	≥6	≥10−2	≥10−4
Target	E-value	1	8	11	15	16	12	17	71	45
K103	# ions	0	0	76	4	0	0	0	80	0
	Hyperscore	0	0	76	4	0	0	0	80	0
	Convolution	0	8	70	2	0	0	0	72	0
	E-value	0	0	76	4	0	0	0	80	0
K104	# ions	0	0	0	80	0	0	0	80	0
	Hyperscore	0	0	0	80	0	0	0	80	0
	Convolution	0	5	44	31	0	0	0	75	0
	E-value	0	0	0	80	0	0	0	80	0
K105	# ions	0	0	0	0	80	0	0	80	80
	Hyperscore	0	0	0	0	80	0	0	80	80
	Convolution	0	3	36	32	9	0	0	77	9
	E-value	0	0	0	0	80	0	0	80	80
K106	# ions	0	0	0	0	1	79	0	80	80
	Hyperscore	0	0	0	0	0	80	0	80	80
	Convolution	0	4	30	36	5	5	0	76	10
	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.

^bSignificance threshold (t) for target spectrum to be considered significant at significance thresholds <1×10^−t (t = 0 to > = 6).

^cThe cumulative number of peptides at 1×10⁻² and 1×10⁻⁴ thresholds.