The most up to date documentation is in the usage text of the conversion
application msconvert (read by running it with no arguments). The first section
is:
Usage: msconvert [options] [filemasks]
Convert mass spec data file formats.
Return value: # of failed files.
Options:
-f [ --filelist ] arg : specify text file containing filenames
-o [ --outdir ] arg (=.) : set output directory [.]
-c [ --config ] arg : configuration file (optionName=value)
-e [ --ext ] arg : set extension for output files
[mzML|mzXML|mgf|txt]
--mzML : write mzML format [default]
--mzXML : write mzXML format
--mgf : write Mascot generic format
--text : write ProteoWizard internal text format
--ms2 : write MS2 format
--cms2 : write CMS2 format
-v [ --verbose ] : display detailed progress information
--64 : set default binary encoding to 64-bit precision
--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 ] arg : 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
Hope this helps,
-Matt
On 7/7/2010 2:20 PM, Jesse J wrote:
ProteoWizard seems to have poor documentation, because I don't see how
to do it
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