Masshunter Quantitative Analysis Method based on Identified Compounds in Qualitative Analysis

After I analyzed a (single or multiple) data files in the Masshunter Qualitative Analysis, I would like to "write" a quantitative method to integrate, quantifey, etc. a larger batch of sample in the Quantitative Analysis Software - without having to re-identify all compounds during the method setup again.

I spent a week going through the provided eFamiliarization program, manuals and online tutorials without finding a working solution to this. At least I have three ideas how it could be implemented, however both of them don't  (fully) work on our newly installed GC/MSD (single quad) system:

- the best option seems to  "Initiate quantification" directly from the Qualitative Analysis software, but this action opens the quantification software for the QQQ instead of SQ method setup and classical interface instead of the Quant-My-Way. Can thgis be changed?

- Second best option: export the analyzed data into a CEF file and build a method from this. However, the number of qualifiers is preset to two, but I would like to include more. Can this be changed?

- Work-around I could live with: export each to be included spectrum into a PCDL, however the PCDL manager is not installed and I can't find it on any of the provided installation media.

Thanks for any help!

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  • Hello ,

    While Initiate quantification does launch the QQQ version of quant, it does appear to make a valid MS scan method. In limited testing I was able to save this method, close quant, launch MS quant, create a new batch, and then apply the saved method to the batch. Though this will only make two qualifiers per target. For some low mass compounds with simple spectrum, it may only assign one qualifier. I’m not aware of any way to change the number of qualifiers made using this option or from method creation using CEF file.

    PCDL is mainly for accurate mass LCMS libraires, and the Export spectrum to PCDL is used for accurate mass MSMS libraries.

    The only ways I know to specify more than two qualifiers when making a quant method is either using the export components feature in Unknowns Analysis, or using the New Method from Acquired Scan Data with Library Search option in quant. I realize that neither of these avoids re-finding the compounds you have already found in qual, but these dialogs will allow you to specify the number of qualifiers per target.

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  • Hello ,

    While Initiate quantification does launch the QQQ version of quant, it does appear to make a valid MS scan method. In limited testing I was able to save this method, close quant, launch MS quant, create a new batch, and then apply the saved method to the batch. Though this will only make two qualifiers per target. For some low mass compounds with simple spectrum, it may only assign one qualifier. I’m not aware of any way to change the number of qualifiers made using this option or from method creation using CEF file.

    PCDL is mainly for accurate mass LCMS libraires, and the Export spectrum to PCDL is used for accurate mass MSMS libraries.

    The only ways I know to specify more than two qualifiers when making a quant method is either using the export components feature in Unknowns Analysis, or using the New Method from Acquired Scan Data with Library Search option in quant. I realize that neither of these avoids re-finding the compounds you have already found in qual, but these dialogs will allow you to specify the number of qualifiers per target.

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