Martin,
Not entirely sure what you want to do but this might be of help.

I'm not using mzmine currently but xcms, which we use to read mzXML files.
The mzXML files were converted from the RAW files using  the tools 'readw' , 
'sed' and 'MzXMLParser' .
For example: to convert positive specific scans:

C:\_myComputer\AMC\Projects\2012\Metabolomics\ReAdW-4.3.1\ReAdW --mzXML 
--verbose .\20120808clpl63.RAW .\20120808clpl63.mzXML
C:\_myComputer\AMC\Projects\2012\Metabolomics\ReAdW-4.3.1\ReAdW --mzXML 
--verbose .\20120808clpl67.RAW .\20120808clpl67.mzXML
C:\_myComputer\AMC\Projects\2012\Metabolomics\ReAdW-4.3.1\ReAdW --mzXML 
--verbose .\20120808clpl71.RAW .\20120808clpl71.mzXML

"C:\Program Files\GnuWin32\bin\sed.exe" -i -e "s/msLevel=\"0\"/msLevel=\"1\"/" 
*.mzXML

java -jar 
C:\_myComputer\AMC\Projects\2012\Metabolomics\MzXMLParser\bin\MzXMLParser17.jar 
20120808clpl63.mzXML split
java -jar 
C:\_myComputer\AMC\Projects\2012\Metabolomics\MzXMLParser\bin\MzXMLParser17.jar 
20120808clpl67.mzXML split
java -jar 
C:\_myComputer\AMC\Projects\2012\Metabolomics\MzXMLParser\bin\MzXMLParser17.jar 
20120808clpl71.mzXML split

hope this helps
antoine

| Prof dr Antoine H.C. van Kampen | (1) Bioinformatics Laboratory | Clinical 
Epidemiology, Biostatistics and Bioinformatics (KEBB) | Academic Medical Center 
(AMC) | Visiting address: Meibergdreef 9, J1B-208 (J-building, floor 1B) | 
Postal address: PO Box 22700, 1100 DE  Amsterdam, the Netherlands | 
www.bioinformaticslaboratory.nl<http://www.bioinformaticslaboratory.nl/> | (2) 
Biosystems Data Analysis | Swammerdam Institute for Life Sciences (SILS) | 
University of Amsterdam | Visiting address:  Science Park 904, C2-208 | 1098 XH 
Amsterdam, The Netherlands | www.bdagroup.nl<http://www.bdagroup.nl/> |phone:   
++31-20-5667096 (AMC) |Mobile:  06-41768067 | 
a.h.vankam...@amc.uva.nl<mailto:a.h.vankam...@amc.uva.nl> | 
Skype:antoine.van.kampen |

From: Martin Lewitt [mailto:martin.lew...@veritomyx.com]
Sent: 12 October 2012 14:32
To: Developer discussion
Subject: [Mzmine-devel] Is there a way to export "raw" files?

mzmine-devel,

I don't see a way to export "raw" files under the raw files menu.  It would be 
helpful to be able to export intermediate results that get stored as raw files 
for evaluation or processing by other software.  If the facility doesn't exist 
would it be easy to implement?  I envision retaining the scan structure in an 
XML or mzXML format, and a possible stretch goal of being able to export just 
selected scans.

regards,
  Martin Lewitt
  martin.lew...@veritomyx.com<mailto:martin.lew...@veritomyx.com>

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