Software:MzXML2Search
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| Options are: | Options are: | ||
| - | -dta or -mgf or -pkl or -xdta or -odta or -ms2 output format (default dta) | + | -dta or -mgf or -pkl or -xdta or -odta or -ms2 output format (default dta) |
| - | -F<num> where num is an int specifying the first scan | + | -F<num> where num is an int specifying the first scan |
| - | -L<num> where num is an int specifying the last scan | + | -L<num> where num is an int specifying the last scan |
| -C<n1>[-<n2>] "force charge(s)": where n1 is an integer specifying the precursor charge state (or possible charge range from n1 to n2 inclusive) to use; this option forces input scans to be output with the user-specified charge (or charge range) | -C<n1>[-<n2>] "force charge(s)": where n1 is an integer specifying the precursor charge state (or possible charge range from n1 to n2 inclusive) to use; this option forces input scans to be output with the user-specified charge (or charge range) | ||
| -c<n1>[-<n2>] "suggest charge(s)": for scans which do not have a precursor charge (or charge range) already determined in the input file, use the user-specified charge (or charge range) for those scans. Input scans which already have defined charge (or charge range) are output with their original, unchanged values. | -c<n1>[-<n2>] "suggest charge(s)": for scans which do not have a precursor charge (or charge range) already determined in the input file, use the user-specified charge (or charge range) for those scans. Input scans which already have defined charge (or charge range) are output with their original, unchanged values. | ||
Revision as of 18:29, 24 May 2010
Description
Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files.
Getting the Software
Comes with the current version of TPP.
Running
MzXML2Search [options] *.mzXML
Options are:
-dta or -mgf or -pkl or -xdta or -odta or -ms2 output format (default dta) -F<num> where num is an int specifying the first scan -L<num> where num is an int specifying the last scan
-C<n1>[-<n2>] "force charge(s)": where n1 is an integer specifying the precursor charge state (or possible charge range from n1 to n2 inclusive) to use; this option forces input scans to be output with the user-specified charge (or charge range) -c<n1>[-<n2>] "suggest charge(s)": for scans which do not have a precursor charge (or charge range) already determined in the input file, use the user-specified charge (or charge range) for those scans. Input scans which already have defined charge (or charge range) are output with their original, unchanged values. -B<num> where num is a float specifying minimum MH+ mass, default=600.0 Da -T<num> where num is a float specifying maximum MH+ scan, default=4200.0 Da -P<num> where num is an int specifying minimum peak count, default=5 -I<num> where num is a float specifying minimum threshold for peak intensity, default=0.01 -M<n1>[-<n2>]where n1 is an int specifying MS level to export (default=2) and n2 specifies an optional range of MS levels to export -A<str> where str is the activation method, "CID" (default) or "ETD" if activation method not in scans of mzXML file, this option is ignored -h use hydrogen mass for charge ion (default is proton mass)
For example:
MzXML2Search .mgf example.mzXML
