Table 1:

Variables and their definitions.

Variable	Definition
Ʃ	set of all spectra (observed)
n	number of spectra (observed)
$\mathcal{D}$t	target database of peptides (user determined)
${\mathcal{D}}_i^d$	decoy database of peptides (user determined)
nd	number of competing decoy database (user determined)
ρ	score threshold (user determined)
D (ρ)	number of decoy discoveries (at level ρ) in a search of the concatenated database $\mathcal{D}$t ∪ $\mathcal{D}$d (observed)
T (ρ)	number of target discoveries (at level ρ) in a search of the concatenated database $\mathcal{D}$t ∪ $\mathcal{D}$d (observed)
σ	single spectrum (observed)
w (σ)	score of the best match of σ in the target database (observed)