Software:MzXML2Search
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| -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 | + | -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) |
| - | specifying the precursor charge state (or possible | + | -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. |
| - | 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 | -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 | -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 | -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 | -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) | + | -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 |
| - | 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 |
| - | -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) | -h use hydrogen mass for charge ion (default is proton mass) | ||
Revision as of 18:28, 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
