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MSCONVERT (1) General Commands Manual MSCONVERT (1)


msconvert — Convert mass spectrometry data file formats.


msconvert [options] [filemasks]


This manual page documents briefly the msconvert software shipped within the libpwiz-tools package. This program allows one to convert mass spectrometry data files from one format to another. Since this version is built on the Free Software Debian platform, only conversions involving Free Software can be performed [that is, *not* involving proprietary Microsoft Windows-based dynamic linking libraries (dlls)].


Display detailed processing progress information.

Show this message, with extra detail on filter options.

Uses the contents of filename which lists filenames.

Set the output directory ('-' for stdout) to dir. By default, the output directory is '.' (that is, the current working directory).

Set the configuration file to filename.

Override the name of the output file.

Set the extension of the output files to ext. Can be mzML or mzXML or mgf or txt.

Write mzML format (default).

Write mzXML format.

Write mgf Mascot generic format.

Write ProteoWizard internal text format.

Write MS1 format.

Write CMS1 format.

Write MS2 format.

Write CMS2 format.

Set default binary encoding to 64-bit precision (default).

Set default binary encoding to 32-bit precision.

Encode m/z values in 64-bit precision (default).

Encode m/z values in 32-bit precision.

Encode intensity values in 64-bit precision.

Encode intensity values in 32-bit precision (default).

Do not write index.

Use filename for contact info.

Use zlib compression for binary data.

gzip entire output file (adds .gz to filename).

Add a spectrum list filter.

Create a single output file from multiple input files by merging file-level metadata and concatenating spectrum lists.

Write selected ion monitoring as spectra, not chromatograms.

Write selected reaction monitoring as spectra, not chromatograms.


Convert data.RAW to data.mzXML

msconvert data.RAW --mzXML

Put output file in my_output_dir

msconvert data.RAW -o my_output_dir

Extract scan indices 5...10 and 20...25

msconvert data.RAW --filter "index [5,10] [20,25]"

Extract MS1 scans only

msconvert data.RAW --filter "msLevel 1"

Extract MSn scans for n>1

msconvert data.RAW --filter "msLevel 2-"

Use a configuration file

msconvert data.RAW -c config.txt


The number of failed files.


Filippo Rusconi <>

This manual page was written by Filippo Rusconi <> (initial writing 05 december 2013). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation.

On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.