Hi! Geert When I asked the same question this February, Gavin kindly suggested the use of a proteowizard tool, msconvert that extracts positive and negative MS1 scans separately. I have tried to use the msconvert tool. Just type msconvert without any additional texts in the Windows command prompt. You can see the usages and examples for msconvert.. After several trials I could successfully get the data separately. A successful text is: msconvert thermo.raw -o destination_directory --outfile file_name --filter "polarity positive" --filter "msLevel 1" To keep MS^n scans in the output, type as follows: msconvert thermo.raw -o destination_directory --outfile file_name --filter "polarity positive" Note: In the option --outfile, a previous file is overwritten by a new file without any caution.
When msconvert sometimes ignores a filter of multiple filters used, MZmine 2 could not open the resultant file and an popup "Error parsing maML: java.lang.NullPointerException (null:-1)" was shown. But, OpenMS could open the same file. I guess that OpenMS would not strictly follow the mzML convention???? Best regards Hiro -------------------------------------------------- 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
