msconvert(1) 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 <[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'.