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)].
- -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 <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'.