Software:MzXML2Search

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Revision as of 18:26, 24 May 2010
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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
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