msconvert - Online in the Cloud

PROGRAM:

NAME

msconvert — 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.

Use msconvert online using onworks.net services