cleanSpectra: This function is used to clean MS2 spectra in different ways....

In michaelwitting/masstrixR: Annotation of MS based metabolomics data

Description

This function is used to clean MS2 spectra in different ways. First, if the MS2 contains "fragment" m/z values above the precursor m/z (option "removeAbovePrecursor"). Second, isotopic peaks in the MS2 spectra can be removed ("isotopeFilitering"). Lastly, peaks below a certain treshold are removed ("tresholdFiltering").

Usage

cleanSpectra(x, cleanFunction = "removeAbovePrecursor", treshold,
  precursorDistance = 5, mzTol = 0.005, mzTolType = "abs")

Arguments

x	A Spectrum2 object to work on
cleanFunction	A string either "removeAbovePrecursor", "isotopeFiltering" or "tresholdFiltering"
precursorDistance	A double indicating from which point above which "fragments" should be removed
mzTol	Maximum allowed tolerance in Da or ppm
mzTolType	Defines the error type for m/z search, "abs" is used for absolute mass error, "ppm" for relative error

michaelwitting/masstrixR documentation built on Nov. 8, 2019, 8:12 p.m.