idconvert(1) Convert mass spectrometry identification file formats.


idconvert [options] [filemasks]


This manual page documents briefly the idconvert software shipped within the libpwiz-tools package. This program allows one to convert mass spectrometry protein identification data files from one format to another.


-v | --verbose
Display detailed processing progress information.
-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.
-e | --ext ext
Set the extension of the output files to ext. Can be mzid or pepXML or txt.
Write mzIdentML format (default).
Write pepXML format.
Write hierarchical text format.


Convert sequest.pepXML to sequest.mzid

idconvert sequest.pepXML

Convert mascot.mzid to mascot.pepXML

idconvert mascot.mzid --pepXML

Use a configuration file

idconvert xtandem.pep.xml -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'.