mergeMS2spectra: Merge MS2 spectra with or without external peak table

In tdepke/CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Merge MS2 spectra with or without external peak table

Description

mergeMS2spectra is used to merge MS2 spectra that come from the same precursor. It does so either by grouping spectra of the same precursor m/z that fall into a defined retention time window (rt_tolerance) or by grouping spectra to peaks from an externally supplied peak table. Please see the vignette for more details.

Usage

mergeMS2spectra(ms2list, mz_tolerance = 1e-05, rt_tolerance = 30,
    peaktable = NULL, exclude_unmatched = FALSE)

Arguments

ms2list	A list of MS2spectrum objects to be merged.
mz_tolerance	The m/z tolerance to be used for merging, default is 1e-5, i.e. +/- 10ppm. If the mass-to-charge ratios of two peaks differ less than mz_tolerance, they are assumed to have the same m/z
rt_tolerance	The retention time tolerance used for merging features. If used without a peak table, rt_tolerance is the maximum retention time difference between to subsequent spectra of the same precursor m/z with which they are still assumed to belong to the same feature If used with an external peak table, rt_tolerance is the maximum retention time difference between a spectrum and a peak in the peak table with which the spectrum is still considered to belong to that peak.
peaktable	An external peak table, e.g. from XCMS, that serves as a template for grouping spectra. The peaktable must be a three-column data.frame with feature ID, m/z and retention time for each peak/feature.
exclude_unmatched	If an external peak table is used: Should spectra that do not match to any peak/feature in the peak table be exclude from the resulting list?

Value

A merged list of MS2spectrum objects.

Examples

my_spectra <- extractMS2spectra(MSfile = system.file("extdata",
                                "PoolA_R_SE.mzXML",
                                package = "CluMSIDdata"),
                                min_peaks = 4, RTlims = c(0,5))

my_merged_spectra <- mergeMS2spectra(my_spectra, rt_tolerance = 20)

tdepke/CluMSID documentation built on April 10, 2022, noon