spectral_entropy_similarity_score {IDSL.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, 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)