MSCONVERT

1 msconvert

msconvert

Convert mass spectrometry data file formats.

          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`'.