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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