msconvert.1

       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'.

                                                                                               MSCONVERT     (1)

       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)].

       Convert data.RAW to data.mzXML

       msconvertdata.RAW--mzXML

       Put output file in my_output_dir

       msconvertdata.RAW-omy_output_dir

       Extract scan indices 5...10 and 20...25

       msconvertdata.RAW--filter"index[5,10][20,25]"

       Extract MS1 scans only

       msconvertdata.RAW--filter"msLevel1"

       Extract MSn scans for n>1

       msconvertdata.RAW--filter"msLevel2-"

       Use a configuration file

       msconvertdata.RAW-cconfig.txt

msconvert      —       Convert mass spectrometry data file formats.

       -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.

       The number of failed files.

msconvert [options][filemasks]