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!

  • Hi I moved your question to the Mass Spectrometry Software Forum for better visibility.  Thanks!

  • I'm not sure about PCDL manager, however if you want to use Library editor to create a custom library it is quite easy to add the individual spectra.

    Open Library Editor (Path on my PC is: "C:\Program Files\Agilent\MassHunter\Workstation\Quant\bin\LibraryEdit.exe") then create a new Library, or if you have one made in file format of mslibrary.xml, open that library. 

    Add a new compound and fill in the details as fully as possible. Once compound data has been added, click the button for "New Spectrum", also click the "Properties" button in the Spectrum View pane. 

    Open your data in Qual, integrate and extract peak spectra for the data file. Personally, I prefer to simply run the Method Workflow and proceed from there.

    From this step, you can:

    • Right click on the identified spectrum and use "Send Spectra to PCDL"
    • Right click on the Spectrum in the MS Spectrum Results pane, click "Export" then send to a delimited file for manual manipulation
    • Select the spectrum then go to the "MS Spectrum Peak List 1" pane, set columns to "m/z" and "Abund", select all the lines (Click on the first line, hold down "SHIFT" then click the last line), right click and either use "Export" or "Copy to Clipboard".

    Regardless of chosen export or copy to clipboard is used, you will need to open in a spreadsheet application to manipulate. You need to have the m/z in first column and Abundance value in second column. If using Excel, use the "Text Import Wizard" so your copied data is split into separate columns.

    Copy the lines with numerical values only (exclude header line) and then go to Library Editor. You have already created the compound, added a blank spectrum, and opened the properties window. The first line of the properties is "Abundance Values", click this line and then the button with ellipses points that appears on the right. This will open a second window titled "Spectrum" with several buttons, click the one labeled "Paste Table", then click "OK". Fill in any data as you see fit (at minimum will want to include Acquired Retention Time, Origin, and Sample ID).

    Repeat process of adding compound and spectrum for each of your desired compounds. Save the library and move to Quant.

    In Quant:

    Create new method from acquired scan data with library search.

    In library method, use the newly created library that only has your compounds of interest as primary. Select a sample and set number of qualifiers as desired. Proceed as normal for creation of a quantitative method.

    The process looks overly complicated in text only format, however it is quite easy and quick to complete.

    Best of luck!

  • 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.

  • Hi ,

    Another way to bring an EI spectrum into the Library Editor from Qual is to right click on the spectrum and choose Copy to Clipboard. Then in the Library Editor you can select the compound, right click in the blank spectrum pane and choose Paste. You can right click and use Filter Peaks to remove any spectral peaks with very low abundance. Just be sure that only one spectrum is selected in Qual, otherwise you will paste multiple spectra into the library. 

  • Hi ,

    I just wanted to follow-up to see if you were able to find a solution to your issue. If so, please come back to the post, let us know what you found, and click Verify Answer on the response so it will make the solution more visible.  If you still need help, just let us know and we would be happy to continue working with you.

  • Yes, I ended up using the library editor and create custom libraries for each experiment, to use these then to create a quan method.

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