spectral_entropy_similarity_score: Spectral Entropy Calculator

In IDSL.FSA: Fragmentation Spectra Analysis (FSA)

Spectral Entropy Calculator

Description

This module measures similarity of spectral entropies between 'PEAK_A' and 'PEAK_B' fragment spectra using a method described by the reference paper.

Usage

spectral_entropy_similarity_score(PEAK_A, S_PEAK_A, PEAK_B, S_PEAK_B, massError,
allowedNominalMass = FALSE)

Arguments

PEAK_A	A matrix (m/z, int) of fragmentation spectra
S_PEAK_A	Spectral entropy of PEAK_A
PEAK_B	A matrix (m/z, int) of fragmentation spectra
S_PEAK_B	Spectral entropy of PEAK_B
massError	Mass accuracy in Da
allowedNominalMass	c(TRUE, FALSE). Select 'TRUE' only for nominal mass analysis.

Value

spectral entropy similarity between 0 - 1

References

Li, Y., Kind, T., Folz, J., Vaniya, A., Mehta, S.S. and Fiehn, O. (2021). Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification. Nature methods, 18(12), 1524-1531, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41592-021-01331-z")}

Examples

allowedWeightedSpectralEntropy <- TRUE
##
A <- cbind(seq(50, 160, length.out = 10), seq(10, 90, length.out = 10))
sA <- spectral_entropy_calculator(A, allowedWeightedSpectralEntropy)
S_PEAK_A <- sA[[1]]
PEAK_A <- sA[[3]]
##
B <- cbind(seq(50, 160, length.out = 10), seq(50, 60, length.out = 10))
sB <- spectral_entropy_calculator(A, allowedWeightedSpectralEntropy)
S_PEAK_B <- sB[[1]]
PEAK_B <- sB[[3]]
##
allowedNominalMass = TRUE
entropyScore <- spectral_entropy_similarity_score(PEAK_A, S_PEAK_A, PEAK_B,
S_PEAK_B, allowedNominalMass)

IDSL.FSA documentation built on July 9, 2023, 6:45 p.m.