.TH "      \fBMSCONVERT\fP     " "1" 
.SH "NAME" 
\fBmsconvert\fP      \(em       Convert mass spectrometry data file formats. 
 
.SH "SYNOPSIS" 
.PP 
\fBmsconvert\fR [\fB\fIoptions\fR\fP]  [\fB\fIfilemasks\fR\fP]  
.SH "DESCRIPTION" 
.PP 
This manual page documents briefly 
the \fBmsconvert\fR software shipped within the 
\fBlibpwiz-tools\fP 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)]. 
 
.SH "OPTIONS" 
.IP "\-v | \-\-verbose" 10 
Display detailed processing progress information. 
 
.IP "\-\-help" 10 
Show this message, with extra detail on filter options. 
 
.IP "\-f | \-\-filelist \fIfilename\fR" 10 
Uses the contents of \fIfilename\fR which lists filenames. 
 
.IP "\-o | \-\-outdir \fIdir\fR" 10 
Set the output directory ('\-' for stdout) to \fIdir\fR. By default, the output directory is '.' (that is, the current working directory). 
 
.IP "\-c | \-\-config \fIfilename\fR" 10 
Set the configuration file to \fIfilename\fR. 
 
.IP "\-\-outfile \fIfilename\fR" 10 
Override the name of the output file. 
 
.IP "\-e | \-\-ext \fIext\fR" 10 
Set the extension of the output files 
to \fIext\fR. Can 
be mzML or mzXML or mgf or txt. 
 
.IP "\-\-mzML" 10 
Write \fBmzML\fP format (default). 
 
.IP "\-\-mzXML" 10 
Write \fBmzXML\fP format. 
 
.IP "\-\-mgf" 10 
Write \fBmgf\fP Mascot generic format. 
 
.IP "\-\-text" 10 
Write ProteoWizard internal \fBtext\fP format. 
 
.IP "\-\-ms1" 10 
Write \fBMS1\fP format. 
 
.IP "\-\-cms1" 10 
Write \fBCMS1\fP format. 
 
.IP "\-\-ms2" 10 
Write \fBMS2\fP format. 
 
.IP "\-\-cms2" 10 
Write \fBCMS2\fP format. 
 
.IP "\-\-64" 10 
Set default binary encoding to 64-bit precision (default). 
 
.IP "\-\-32" 10 
Set default binary encoding to 32-bit precision. 
 
.IP "\-\-mz64" 10 
Encode m/z values in 64-bit precision (default). 
 
.IP "\-\-mz32" 10 
Encode m/z values in 32-bit precision. 
 
.IP "\-\-inten64" 10 
Encode intensity values in 64-bit precision. 
 
.IP "\-\-inten32" 10 
Encode intensity values in 32-bit precision (default). 
 
.IP "\-\-noindex" 10 
Do not write index. 
 
.IP "\-i | \-\-contactInfo \fIfilename\fR" 10 
Use \fIfilename\fR for contact info. 
 
.IP "\-z | \-\-zlib" 10 
Use zlib compression for binary data. 
 
.IP "\-g | \-\-gzip" 10 
gzip entire output file (adds .gz to filename). 
 
.IP "\-\-filter \fIarg\fR" 10 
Add a spectrum list filter. 
 
.IP "\-\-merge" 10 
Create a single output file from multiple input files by merging file-level metadata and concatenating spectrum lists. 
 
.IP "\-\-simAsSpectra" 10 
Write selected ion monitoring as spectra, not chromatograms.  
 
.IP "\-\-srmAsSpectra" 10 
Write selected reaction monitoring as spectra, not chromatograms.  
 
.SH "EXAMPLES" 
.PP 
Convert data.RAW to data.mzXML 
 
.PP 
\fBmsconvert data.RAW \-\-mzXML\fR      
.PP 
Put output file in my_output_dir 
 
.PP 
\fBmsconvert data.RAW \-o my_output_dir\fR      
.PP 
Extract scan indices 5...10 and 20...25 
 
.PP 
\fBmsconvert data.RAW \-\-filter "index [5,10] [20,25]"\fR      
.PP 
Extract MS1 scans only 
 
.PP 
\fBmsconvert data.RAW \-\-filter "msLevel 1"\fR      
.PP 
Extract MSn scans for n>1 
 
.PP 
\fBmsconvert data.RAW \-\-filter "msLevel 2-"\fR      
.PP 
Use a configuration file 
 
.PP 
\fBmsconvert data.RAW \-c config.txt\fR      
.SH "RETURN VALUE" 
.PP 
The number of failed files. 
 
.SH "AUTHOR" 
.PP 
Filippo Rusconi <lopippo@debian.org>  
.PP 
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. 
 
.PP 
On a Debian system the complete text of the GNU General 
Public License version 3 can be found in the file 
`\fB/usr/share/common-licenses/GPL\-3\fP'. 
 
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