extractMS2spectra: Extract MS2 spectra from raw data files

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

Extract MS2 spectra from raw data files

Description

extractMS2spectra() is used to extract MS2 spectra from raw data files, e.g. mzXML files.

Usage

extractMS2spectra(MSfile, min_peaks = 2, recalibrate_precursor = FALSE,
    RTlims = NULL)

Arguments

MSfile	An LC-MS/MS raw data file in one of the non-proprietary formats that can be parsed by mzR, e.g. mzXML or mzML.
min_peaks	Minimum number of peaks in MS2 spectrum, defaults to 2. Spectra with less than min_peaks fragment peaks will be ignored and not extracted.
recalibrate_precursor	Logical, defaults to FALSE. Applicable only for files that were exported to mzXML using a deprecated version of Bruker Compass Xport (< 3.0.13). If set to TRUE, the precursor m/z will be recalculated from the respective fragment m/z in the MS2 spectrum. For details, see Depke et al. 2017.
RTlims	Retention time interval for the extraction of spectra. Provide as numeric vector of length 2. Spectra with retention time < RTlims[1] or > RTlims[2] will be ignored.

Value

A list with objects of class MS2spectrum, containing MS2 spectra extracted from the raw data.

Examples

my_spectra <- extractMS2spectra(MSfile = system.file("extdata",
                                "PoolA_R_SE.mzXML",
                                package = "CluMSIDdata"),
                                min_peaks = 4, RTlims = c(0,10))

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