Optimal precursor ion selection for LC-MALDI MS/MS

BMC Bioinformatics

Table 1 Variables and constants used in LP formulations

Variable name	Explanation
x _j,s	Indicator variable, 1 if feature j is selected in spectrum s,
	0 otherwise
x _j	Indicator variable, 1 if feature j is part of the solution,
	0 otherwise
int _j,s	Normalized signal intensity of feature j in spectrum s
cap _s	Maximal number of MS/MS precursors in spectrum s
D _i	Detectability of protein i
y _i	-log(1-D_i), higher values reflect a better protein detectability
d _k	Detectability of peptide k
a _i,k	Indicator variable, 1 if peptide k is part of protein i,
	0 otherwise
ws	RT window size
t _p	Predicted RT
max_list_size	maximal number of elements in inclusion list
p _k	Probability that peptide k was identified correctly
P _i	Probability that protein i was identified correctly
k₁,k₂,k₃	Weights
b _i	Indicator variable, 1 if the protein probability of protein i is at least c, 0 otherwise
c	Minimal protein probability to declare a protein identified
z _i	z_i = 1 if P_i ≥ c, otherwise z_i ∈ [0, 1)
M _k	Set of features having an m/z within a specified ppm range around the theoretical m/z of peptide k
m _k,j	Matching probability of feature j with peptide k
precs	Number of already fragmented precursors
step_size	Number of selected precursors in each iteration

ISSN: 1471-2105