neutralloss: Calculate similarity based on neutral losses

In MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Description

Calculate similarity based on neutral losses (NLS)

Usage

neutralloss(x, y, m = 0.5, n = 2, ...)

Arguments

x	'Spectrum2' object from 'MSnbase' containing intensity and m/z values, first MS/MS spectrum
y	'Spectrum2' object from 'MSnbase' containing intensity and m/z values, second MS/MS spectrum
m	'numeric', exponent to calculate peak intensity-based weights
n	'numeric', exponent to calculate m/z-based weights
...	further arguments passed to 'MSnbase:::bin_Spectra'

Details

Similarities of spectra based on neutral losses are calculated according to the following formula:

∑(W_{S1, i} \cdot W_{S2, i}) ^ 2 ∑(W_{S1, i} ^ 2) * ∑(W_{S2, i} ^ 2)

, with W = [ peak intensity] ^{m} \cdot [ NL ]^n and NL = | m/z - precursor m/z |. For further information see Li et al. (2015): Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis. PNAS, E4147–E4155. 'neutralloss' returns a numeric value ranging between 0 and 1, where 0 indicates no similarity between the two MS/MS features, while 1 indicates that the MS/MS features are identical. Arguments can be passed to the function 'MSnbase:::bin_Spectra', e.g. to set the width of bins (binSize). Prior to calculating

W_{S1}

or

W_{S2}

, all intensity values are divided by the maximum intensity value.

Value

'neutralloss' returns a numeric similarity coefficient between 0 and 1

Author(s)

Thomas Naake, [e-mail]

Examples

data("spectra", package = "MetCirc")
x <- spectra_tissue[[1]]
y <- spectra_tissue[[2]]
neutralloss(x, y, m = 0.5, n = 2, binSize = 0.01)

MetCirc documentation built on Nov. 8, 2020, 8:26 p.m.