Hi! Follow up info. I noticed that MZmine 2 can not open some mzML files processed by msconvert, even when msconvert seemed to work normally. My data contain alternate positive and negative MS1 scans over the whole elution time, and in addition, MS2 and MS3 scans of one polarity desired during a certain reterntion time window (event time). In the test cases, MZmine 2 can open mzML files that contain only MS1 data of either polarity and MS1-MS3 data in the negative ion mode, but cannot open a mzML file containing MS1-MS3 data in the positive ion mode [SEVERE|WorkerThread]: Task error: Error parsing mzML: java.lang.NullPointerException (null:-1)].. openMS can open the same file again.
Please let me know which parts of the mzML file structure I should check to make sure why these happen. Best regards Hiro ************************************* Hiromasa Tojo hirog...@hotmail.com Dept. of Biochemistry and Molecular Biology Osaka University Graduate School of Medicine 2-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN ht...@mr-mbio.med.osaka-u.ac.jp Tel: +81-6-6879-3427 Fax: +81-6-6879-3428 ************************************* -------------------------------------------------- From: "gegoe" <ge...@psb.vib-ugent.be> Sent: Friday, March 09, 2012 2:46 AM To: <mzmine-devel@lists.sourceforge.net> Subject: Re: [Mzmine-devel] how to extract positive and negative MS1 scan data separately from a single Thermo raw file that contains MS1 data in both positive and negative modes. > Hi, I have the same problem, ok, for the msconvertor, but how to do it?? > > Any succes, or anyone can tell me how to do it? > > cheers, > geert. > > -- > View this message in context: > http://mzmine-devel-developer-discussion.970458.n3.nabble.com/Mzmine-devel-how-to-extract-positive-and-negative-MS1-scan-data-separately-from-a-single-Thermo-raw--tp3759817p3810345.html > Sent from the Mzmine-devel -- Developer discussion mailing list archive at > Nabble.com. > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel > ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
