Software:MzXML2Search
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- | Options are: | + | Options: |
- | -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. |
- | -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) and n2 specifies an optional range of MS levels to export | + | ;-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 | + | ;-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) |
For example: | For example: |
Revision as of 18:39, 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:
- -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