Raw MS file conversion

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	# Convert RAW files using msconvert with centroiding		# Convert RAW files using msconvert with centroiding
	# msconvert runs only on themis.		# msconvert runs only on themis.
-	remoteconvert.pl --convertWith msconvert --mzXML --filter 'peakPicking [1,2]' --server THEMIS	+	# (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?		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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Revision as of 15:05, 16 October 2009

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
# msconvert runs only on themis.
# (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?