Software:MzXML2Search
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| ==Description== | ==Description== | ||
| + | Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files. | ||
| + | ==Getting the Software== | ||
| + | Comes with the current version of TPP. | ||
| ==Running== | ==Running== | ||
| + | <pre> | ||
| + | MzXML2Search [options] *.mzXML | ||
| + | </pre> | ||
| + | |||
| + | Options are: | ||
| + | |||
| + | 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: | ||
| + | <pre> | ||
| + | MzXML2Search .mgf example.mzXML | ||
| + | </pre> | ||
Revision as of 18:24, 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:
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
