msconvert {MetabolomicsBasics}

msconvert.

Description

msconvert is calling ProteoWizards MSConvert as a command line tool on Windows.

Usage

msconvert(
  files = NULL,
  msc_exe =
    "C:\\Program Files\\ProteoWizard\\ProteoWizard 3.0.11856\\msconvert.exe",
  args = c("--filter \"peakPicking cwt snr=0.01 peakSpace=0.1 msLevel=1\"",
    "--filter \"scanTime [0,3600]\"", "--filter \"metadataFixer\"", "--mzML", "--32",
    "--zlib")
)

Arguments

files

A character vector of MS data files (wiff, raw, d, ...).

msc_exe

The path to the installed 'msconvert.exe'.

args

The arguments passed to msconvert on the command line (see details for documentation).

Details

It is a quick and dodgy function to show how to convert vendor MS data into an open format (mzML). You will have to download/install MSConvert prior to usage, and probably adjust the arguments according to your needs. Arguments are documented here https://proteowizard.sourceforge.io/tools/msconvert.html. If you don't know where the msconvert.exe is installed you can check for the correct path using list.files(path="C:/", pattern="^msconvert.exe$", recursive = TRUE).

Value

Only some informative outputs printed to the console. The specified MS data files will be converted to mzML within the same folder.