EIC and MS2 Plotting from Mass List — generate_eic

This function will search for a given list of m/z values in all mzML files within a specified directory. For those found, it will generate an extracted ion chromatograph and individual MS2 spectra for each peak within that chromatograph. Tables of retention times and intensities will be generated for EIC plots, tables of fragment m/z and intensities will be generated for corresponding MS2 spectra.

Usage

generate_eic_ms2(
  path_to_files,
  mass_list,
  out.dir = NA,
  ppm_tolerance = 0,
  da_tolerance = 0,
  pct_int_filt = 0.01,
  min_filt = 10000,
  window = 10,
  keep_log = TRUE
)

Arguments

path_to_files: Path to the directory containing mzML files to be analyzed.
mass_list: A vector containing unique m/z values for use in search.
out.dir: Directory to be used for results, if none is specified then a new directory 'results' will be generated. Default is NA.
ppm_tolerance: Mass tolerance in parts-per-million. Either this value or da_tolerance must be specified. The broadest resulting mass window will be used. Default is 0.
da_tolerance: Mass tolerance in Dalton. Either this value or ppm_tolerance must be specified. The broadest resulting mass window will be used. Default is 0.
pct_int_filt: Threshold where intensities below this fraction of the maximum intensity will not be considered when calculating local maxima within EICs. Default is 0.01 (1%).
min_filt: Baseline intensity below which will not be considered when calculating local maxima within EICs. Default is 1e4.
window: Window size for rolling maximum used in peak detection. Default is 10.
keep_log: Whether or not to preserve the generated log file. Default is TRUE.

Value

A matrix with file-mz pairs and the number of detected peaks.