filterFourierTransformArtefacts: Fast fourier transform artefact filter

In rformassspectrometry/Spectra: Spectra Infrastructure for Mass Spectrometry Data

Fast fourier transform artefact filter

Description

The filterFourierTransformArtefacts() function removes (Orbitrap) fast fourier artefact peaks from spectra. Such artefacts (also referred to as ripples) seem to be related to the ringing phenomenon and are frequently seen in Orbitrap data as small random mass peaks ~ 0.01 Da from a main peak with a very large intensity. See also here for more details and information. The data set fft_spectrum represents a Spectra() object with a single Orbitrap spectrum with such artefacts (see examples below).

See also Spectra() (section *Data subsetting, filtering and merging) for the definition of the function.

Details

The current implementation iterates through all intensity ordered peaks in a spectrum and removes all peaks with an m/z within +/- halfWindowSize of the current peak if their intensity is lower than threshold times the current peak's intensity. Additional parameters keepIsotopes, maxCharge and isotopeTolerance allow to avoid removing of potential ⁠[13]C⁠ isotope peaks (maxCharge being the maximum charge that should be considered and isotopeTolerance the absolute acceptable tolerance for matching their m/z).

Author(s)

Jan Stanstrup, Johannes Rainer

Examples

library(Spectra)
data(fft_spectrum)

plotSpectra(fft_spectrum)

## Focus on an artefact
plotSpectra(fft_spectrum, xlim = c(264.5, 265.5))
plotSpectra(fft_spectrum, xlim = c(264.5, 265.5), ylim = c(0, 5e6))

fft_spectrum <- filterFourierTransformArtefacts(fft_spectrum)
fft_spectrum
plotSpectra(fft_spectrum, xlim = c(264.5, 265.5), ylim = c(0, 5e6))

## R code to download/extract the data.

## Not run: 
library(Spectra)
# get orbitrap data
download.file("https://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS469/AV_01_v2_male_arm1_juice.mzXML", "AV_01_v2_male_arm1_juice.mzXML")
data <- Spectra("AV_01_v2_male_arm1_juice.mzXML")
extracted_spectrum <- data[195]

## End(Not run)

rformassspectrometry/Spectra documentation built on Sept. 27, 2024, 5:43 a.m.