Software:MzXML2Search

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Revision as of 18:30, 24 May 2010 Jesse j (Talk | contribs) (→Running) ← Previous diff		Revision as of 18:39, 24 May 2010 Jesse j (Talk | contribs) (→Running) Next diff →
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	</pre>		</pre>
-	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:

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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