---
name: "msconvert"
section: "1"
platform: "linux"
package: "libpwiz-tools"
version: "3.0.18342-4+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/msconvert"
---

# msconvert(1)

Convert mass spectrometry data file formats.

## NAME

**msconvert**      —       Convert mass spectrometry data file formats.

## SYNOPSIS

**msconvert** \[*options\]  \[filemasks\]*

## DESCRIPTION

*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 \[that is, \*not\* involving proprietary Microsoft  Windows-based dynamic linking libraries (dlls)\].

## OPTIONS

- \-v \| --verbose

  Display detailed processing progress information.

- \--help

  Show this message, with extra detail on filter options.

- \-f \| --filelist *filename*

  Uses the contents of *filename* which lists filenames.

- \-o \| --outdir *dir*

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

- \-c \| --config *filename*

  Set the configuration file to *filename*.

- \--outfile *filename*

  Override the name of the output file.

- \-e \| --ext *ext*

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

- \--mzML

  Write **mzML** format (default).

- \--mzXML

  Write **mzXML** format.

- \--mgf

  Write **mgf** Mascot generic format.

- \--text

  Write ProteoWizard internal **text** format.

- \--ms1

  Write **MS1** format.

- \--cms1

  Write **CMS1** format.

- \--ms2

  Write **MS2** format.

- \--cms2

  Write **CMS2** format.

- \--64

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

- \--32

  Set default binary encoding to 32-bit precision.

- \--mz64

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

- \--mz32

  Encode m/z values in 32-bit precision.

- \--inten64

  Encode intensity values in 64-bit precision.

- \--inten32

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

- \--noindex

  Do not write index.

- \-i \| --contactInfo *filename*

  Use *filename* for contact info.

- \-z \| --zlib

  Use zlib compression for binary data.

- \-g \| --gzip

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

- \--filter *arg*

  Add a spectrum list filter.

- \--merge

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

- \--simAsSpectra

  Write selected ion monitoring as spectra, not chromatograms.

- \--srmAsSpectra

  Write selected reaction monitoring as spectra, not chromatograms.

## EXAMPLES

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**

## RETURN VALUE

The number of failed files.

## AUTHOR

Filippo Rusconi \<lopippo@debian.org\>

This manual page was written by Filippo Rusconi  \<lopippo@debian.org\> (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**'.