Software:MzXML2Search

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Revision as of 18:39, 24 May 2010 Jesse j (Talk | contribs) (→Running) ← Previous diff		Current revision Jesse j (Talk | contribs) (→Running)
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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
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	;-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
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	;-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:
	<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