Software:MzXML2Search

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	-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	+	-C<n1>[-<n2>] "force charge(s)": where n1 is an integer
-	specifying the precursor charge state (or possible	+	specifying the precursor charge state (or possible
-	charge range from n1 to n2 inclusive) to use; this option	+	charge range from n1 to n2 inclusive) to use; this option
-	forces input scans to be output with the user-specified	+	forces input scans to be output with the user-specified
-	charge (or charge range)	+	charge (or charge range)
-	-c<n1>[-<n2>] "suggest charge(s)": for scans which do not have a	+	-c<n1>[-<n2>] "suggest charge(s)": for scans which do not have a
-	precursor charge (or charge range) already determined in the	+	precursor charge (or charge range) already determined in the
-	input file, use the user-specified charge (or charge range)	+	input file, use the user-specified charge (or charge range)
-	for those scans. Input scans which already have defined	+	for those scans. Input scans which already have defined
-	charge (or charge range) are output with their original,	+	charge (or charge range) are output with their original,
-	unchanged values.	+	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"	+	-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	+	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 18:26, 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