msconvert (1)

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)].

-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.

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 <[email protected]>

This manual page was written by Filippo Rusconi <[email protected]> (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'.