mergeMS2spectra: Merge MS2 spectra with or without external peak table
In CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Description Usage Arguments Value Examples

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.

1 2	mergeMS2spectra(ms2list, mz_tolerance = 1e-05, rt_tolerance = 30, peaktable = NULL, exclude_unmatched = FALSE)

`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?

A merged list of MS2spectrum objects.

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)