msconvert: msconvert.

In MetabolomicsBasics: Basic Functions to Investigate Metabolomics Data Matrices

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",
  out_path = NULL,
  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, ...). If unspecified, function will return the args to msconvert.
msc_exe	The path to the installed 'msconvert.exe'.
out_path	Specify valid path or keep NULL to write output in same folder as input.
args	The arguments passed to msconvert on the command line (see details for documentation). Can be a keyword describing a predefined set (currently: 'default' and 'sciex_MS2' are available)

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). You may read on the potential arguments calling msconvert with the argument '–help', system2(command = 'path/to/msconvert.exe', args = "–help").

Value

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

Examples

msconvert()

MetabolomicsBasics documentation built on Dec. 3, 2025, 5:08 p.m.