6 Replies Latest reply on Feb 21, 2018 1:48 PM by ctizaoui

    Export MS2Scan chromatograms into csv format

    ctizaoui

      Hi, How can I export MassHunter data of MS2Scan chromtograms with the full scan spectra included at each time in csv (or text or xls) format?

        • Re: Export MS2Scan chromatograms into csv format
          ryoboyle

          Hello,

           

          I added tags to this post to increase visibility.

           

          Would you mind providing more information? What model MS are you collecting data from? What revision of MassHunter Qual or Quant are you using to open/analyze the data?

            • Re: Export MS2Scan chromatograms into csv format
              ctizaoui

              Thank you for your prompt reply.

               

               

               

              We are using Agilent Triple Quad 6400 series  B.06.00. We use both Qual and Quant version B.06.00, though Qual is more used for data opening and analysis. Hope you cam help with answering my initial question.

               

              thanks

               

              Chedly

                • Re: Export MS2Scan chromatograms into csv format
                  andyg

                  Chedley-

                   

                  The chromatogram is an interpretation of the MS data (IC, BPC, EIC..) so I don't think you can get both out at once. 

                   

                  You can export any chromatogram (TIC, EIC,..) by right-clicking on the chromatogram and selecting Export and then use csv format.

                   

                  You can convert any spectrum to csv in a similar fashion by right clicking on an MS spectrum.

                   

                  I don't know of a way to convert an entire file to csv format partially since a csv format for 3D+ data is not well defnd.  To export MS spectra to a text file (which could be converted to csv format - not necessarily easily), I would use msconvert from ProteoWizard.  It is free and there is a gui version of this software too. 'http://proteowizard.sourceforge.net/downloads.shtml  msconvertgui.exe

                   

                  Andy

                    • Re: Export MS2Scan chromatograms into csv format
                      ctizaoui

                      Hi again Andy,

                       

                       

                       

                      If you don't mind I'll explain what I want to do and you may have a better way on how to extract the information. Basically we collect samples at different times from a developing reaction that produces different products that we don't know. We analyse these samples using the QQQ MS2Scan; the sample passes through a chromatographic column before the ESI. Our aim is to detect all m/z that show changes from one sample to another. Several compounds have the same m/z but possibly different RTs and others have similar RTs but different m/z. Can we use Quant or Qual to automatically detect those m/z that change between samples across all RTs? I appreciate it is a lot of data to look at and I was hoping to extract the raw data and write a vba macro to automatically process it.

                       

                      Thanks again

                       

                      Chedly