Table 2: Variables and their definitions.

Note that there is no overlap between the relevant and irrelevant peptides. Thus, $\mathcal{T}={\mathcal{T}}_r\cup {\mathcal{T}}_i$ and ${\mathcal{T}}_r\cap {\mathcal{T}}_i=\varnothing$. In addition, if neighbor peptides are not defined, then they are considered to be irrelevant. However, if neighbor peptides are defined, then they are considered distinct from irrelevant peptides.

Variable	Definition
S	set of all observed spectra
$\mathcal{T}$	target database of all peptides
$\mathcal{D}$	decoy database of all peptides
${\mathcal{T}}_r$	target database of relevant peptides
${\mathcal{D}}_r$	decoy database of relevant peptides
${\mathcal{T}}_i$	target database of irrelevant peptides
${\mathcal{D}}_i$	decoy database of irrelevant peptides
${\mathcal{T}}_n$	target database of neighbor peptides
${\mathcal{D}}_n$	decoy database of neighbor peptides
α	user defined FDR threshold
α′	user defined filtering FDR threshold
T(s)	number of target PSMs with score better than s
D(s)	number of decoy PSMs with score better than s
Tr(s)	number of relevant target PSMs with score better than s
D(−∞)	total number of decoy PSMs
Tr(−∞)	total number of relevant target PSMs
Dr(−∞)	total number of relevant decoy PSMs
P	set of peptides that result from a database search
M	set of scores that result from a database search
R	set of accepted PSMs
pi	a peptide
mi	precursor mass associated with peptide pi
Bi	number of b- and y-ions associated with peptide pi
Bi,j	number of shared b- and y-ions between peptides pi and pj
tm	mass tolerance to define neighbor peptides
ti	shared ion fraction tolerance to define neighbor peptides