Raw MS file conversion

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Revision as of 15:02, 16 October 2009 Tfarrah (Talk | contribs) ← Previous diff		Current revision Tfarrah (Talk | contribs) (→remoteconvert.pl)
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	# Convert RAW files using msconvert with centroiding		# Convert RAW files using msconvert with centroiding
-	# msconvert runs only on themis.	+	# (The command below did not work for me)
-	remoteconvert.pl --convertWith msconvert --mzXML --filter 'peakPicking [1,2]' --server THEMIS	+	remoteconvert.pl --convertWith msconvert --mzXML --filter 'peakPicking true [1,2]' --server THEMIS
		+
		+	Question on Terry's mind: how can I tell whether my data needs centroiding? Is it bad to centroid data that's already been centroided?

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Current revision

There are several pieces of software to convert raw MS files to XML format (mzXML or mzML). Many of these are proprietary and run only under Windows. Zhi created a global converter that runs under Linux and sends jobs out to Windows boxes:

remoteconvert.pl

This program resides at/regis/sbeams/remoteconvert.pl

Sample invocations:

# View usage information
remoteconvert.pl

# View the options available for each converter
remoteconvert.pl --showOptions

# Convert RAW files to mzXML using ReAdW with centroiding
remoteconvert.pl --default *.RAW

# Convert RAW files using msconvert with centroiding
# (The command below did not work for me)
remoteconvert.pl --convertWith msconvert --mzXML --filter 'peakPicking true [1,2]' --server THEMIS

Question on Terry's mind: how can I tell whether my data needs centroiding? Is it bad to centroid data that's already been centroided?