Software:MzXML2Search

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==Running== ==Running==
 +Note: Though MzXML2Search's usage statement doesn't mention it, MzXML2Search can also convert mzML files.
<pre> <pre>
MzXML2Search [options] *.mzXML MzXML2Search [options] *.mzXML
</pre> </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)
- -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: For example:
<pre> <pre>
-MzXML2Search .mgf example.mzXML+MzXML2Search -.mgf example.mzXML
 +</pre>
 +OR
 +<pre>
 +MzXML2Search -.mgf example.mzML
</pre> </pre>

Current revision

Description

Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files.

Getting the Software

Comes with the current version of TPP.

Running

Note: Though MzXML2Search's usage statement doesn't mention it, MzXML2Search can also convert mzML files.

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

OR

MzXML2Search -.mgf example.mzML
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