Proteome Science

Table 1 Pattern features for net ₁ and net ₂

From: Identification of b-/y-ions in MS/MS spectra using a two stage neural network

*net* ₁ pattern features		*net* ₂ pattern features
feature	value	feature	value
intensity	N, D	intensity	N, D
strong peak	B	strong peak	B
local intensity rank	N	local intensity rank	N
global intensity rank	N	global intensity rank	N
relative cleavage position	N, D	relative cleavage position	N, D
random peak hypothesis	P	random peak hypothesis	P
principal isotope	H	principal isotope	H
isotopologue	B	isotopologue	B
complement	$N$	complement	$P_{{n e t}_{1}}$
H₂O neutral loss	N, D	H₂O neutral loss	N, D
NH₃ neutral loss	N, D	NH₃ neutral loss	N, D
H₂O-H₂O neutral loss	N, D	H₂O-H₂O neutral loss	N, D
H₂O-NH₃ neutral loss	N, D	H₂O-NH₃ neutral loss	N, D
CO neutral loss (a-ion)	N, D	CO neutral loss (a-ion)	N, D
		N-term flanking ion	$P_{{n e t}_{1}}$
		C-term flanking ion	$P_{{n e t}_{1}}$

N specifies a normalized quantity, D specifies a discretized quantity, B indicates a binary value, H indicates a histogram value, $N$ indicates a value sampled from a normal distribution, and P indicates a probability. All peaks are processed first by net ₁ and and then by net ₂. net ₂ features are influenced by the preceding characterization of peaks by net ₁.

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ISSN: 1477-5956

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