2 Replies Latest reply on Jan 17, 2019 8:04 AM by hexatriene

    Problems with [compound MS spectrum results]

    silence

      Data acquired from GC-MS was imported into Masshunter and was deconvolved to find compounds. Next, when I click on that entity, it was showed in [compound MS spectrum results] as :QQ图片20190112051650.png.So, I don't know the difference between the meaning of the two definitions in red circles here. Can I understand that the upper one is the spectrum of the identified compound, and the lower one means every fragment scanned by EI?

       

      Next, I right click and search using NIST-MS program, sometimes it doesn't show valid compounds, unless I double click the area in red circle, why? Do I make a mistake when I use Masshunter or NIST-MS?QQ图片20190112051656.png

       

      Thank you in advance.

        • Re: Problems with [compound MS spectrum results]
          ryoboyle

          Hello,

           

          I added tags to this post to increase visibility.

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          • Re: Problems with [compound MS spectrum results]
            hexatriene

            Hi silence,

            don't know the difference between the meaning of the two definitions in red circles here. Can I understand that the upper one is the spectrum of the identified compound, and the lower one means every fragment scanned by EI?

            Yes - the top spectrum is of the compound as determined by the 'Find by Chromatogram Deconvolution' algorithm. The bottom spectrum is the raw spectrum of the data file averaged over the same time range used in the top spectrum. This is a quick way to determine what ions were identified by the algorithm as belonging together vs. all the ions acquired at that range in time.

            Next, I right click and search using NIST-MS program, sometimes it doesn't show valid compounds, unless I double click the area in red circle, why? Do I make a mistake when I use Masshunter or NIST-MS?

            I believe this is because you need to have a spectrum selected in Qual to "pass" to the NIST software. If you don't have a spectrum selected - NIST will be opened but not have any spectra to process. Selection of a spectrum will result in a blue box drawn around the spectrum as you can see in your first screenshot. Next time you encounter this issue - return to Qual and see if that blue highlighting was present or not. If not - that confirms my suspicion. If so - then we'll need to investigate further.

            ~hexatriene

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