Raw MS file conversion

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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?

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