Table 2. Peptide detection significance levels using experimental spectra of the 103 peptides with and without any post-translational modifications (PTMs) against a standard target database across database search programs (OMSSA, X! Tandem, and Crux).

Program	PTMs			Significancea							Cum Nb
		Missc	Incd	0	1	2	3	4	5	≥6	P≤10−2
X! Tandem	None	0	0	1	8	11	15	16	11	18	71
	Amidation	0	0	0	0	0	0	0	0	9	9
	Oxidation	0	0	0	0	0	0	0	0	1	1
	Pyroglutamination	0	0	0	0	1	0	1	1	1	4
	Phosphorylation	0	0	0	0	0	0	0	1	3	4
	N-terminal acetylation	0	5	0	0	0	0	0	0	0	0
OMSSA	None	0	0	0	0	1	2	1	3	73	80
	Amidation	1	0	1	0	0	0	1	0	6	7
	Oxidation	0	0	0	0	0	0	0	0	1	1
	Pyroglutamination	0	0	0	0	0	0	1	0	3	4
	Phosphorylation	0	0	0	0	0	0	0	0	4	4
	N-terminal acetylation	0	1	0	0	0	0	0	0	4	4
Crux	None	0	0	9	8	9	44	1	0	9	63
	Amidation	0	0	0	1	5	1	1	0	1	8
	Oxidation	0	0	0	0	0	1	0	0	0	1
	Pyroglutamination	0	0	1	1	0	2	0	0	0	2
	Phosphorylation	0	0	0	2	2	0	0	0	0	2
	N-terminal acetylation	0	0	0	1	1	2	0	1	0	4

^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.

^cNumber of peptides missed by program.

^dNumber of peptides with incorrect post-translational modification assignment.