Table 1. Peptide detection significance levels using ideal simulated spectra of the 103 peptides with and without any post-translational modifications (PTMs) and all b- and y-ions including neutral mass losses against a standard target database across database search programs (OMSSA, X! Tandem, and Crux).

Program	PTMs	Significancea							P≤10−2b
		0	1	2	3	4	5	≥6
X! Tandem	None	0	0	4	4	2	6	58	74
	Amidation	0	0	0	0	0	0	9	9
	Oxidation	0	0	0	0	0	0	1	1
	Pyroglutamination	0	0	1	0	1	1	1	4
	Phosphorylation	0	0	0	0	0	1	3	4
	N-terminal acetylation	0	0	0	0	0	0	0	0
OMSSA	None	0	0	0	0	0	0	79	79
	Amidation	0	0	0	0	0	0	9	9
	Oxidation	0	0	0	0	0	0	1	1
	Pyroglutamination	0	0	1	2	1	0	0	4
	Phosphorylation	0	0	0	0	0	0	4	4
	N-terminal acetylation	0	0	0	0	0	0	5	5
Crux	None	2	5	12	52	3	1	2	70
	Amidation	0	0	2	3	2	0	2	9
	Oxidation	0	0	0	1	0	0	0	1
	Pyroglutamination	0	1	1	0	1	0	1	3
	Phosphorylation	0	0	1	2	0	0	1	4
	N-terminal acetylation	0	0	0	3	1	0	1	5

^aSignificance threshold (t) for matched to be considered significant at an E-value or p-value < 1×10^−t (t = 0 to > = 6).

^bCumulative number of peptides with an E-value or p-value < 1×10⁻².