Qualifier ion ratio 'uncertainty' parameter is being ignored for target matching


I am using the MassHunter Quantitative Analysis 10 software to quantify GC-MS data from plant samples, and I have standards and standard curves which I am using to quantify individual compounds.

Some of my standards are not expected to be present in some samples, but they may have peaks at about the same retention time as other compounds. In the case of limonene and beta-phellandrene, they cannot be separated by retention time, but the qualifier ion ratios are different so it is easy to distinguish them.

The problem that I am having is that for a sample which should ONLY have limonene, the software identifies the single limonene peak as both limonene AND beta-phellandrene, even though the qualifier ion ratios are completely out of bounds for beta-phellandrene and they are perfect for limonene.

I have already set all compounds in the method to use "Close RT with qualifiers". I've set up the qualifier ion ratios to have strict uncertainty percentages. The ratios just get highlighted in the results but the peaks are still being identified as the wrong compound. Is there anything else that I can do to prevent misidentification? I don't see a way to specify "minimum number of qualifiers" or anything like that, and I'm getting false-positives for other compounds because of this as well. Even in samples where there are no matching qualifier ions, the software still gives a target match and a concentration.

What have I set up wrong here? Have I overlooked something?


  • Have you shortened your left and right RT delta to exclude the other peak?

  • Unfortunately the compounds share the same retention time (there is a 0.01 minute difference, they would not be resolved as separate peaks with this method).

    If there is a way to disable a compound from being exported, that would work too. I guess I could also delete compounds from the analysis method if I deem them to be not real but that seems like a very roundabout solution.

    This software SHOULD be able to exclude results if my qualifier criteria aren't met, but I don't see a single way to do it. It just spits out colored cell warnings that also can't even be exported.

  • Hello  ,

    The method criteria setting allows you to specify how quant picks the best peak for a target in the identification window. For the Close RT with qualifiers, if there are no peaks that match the qualifier settings then it picks the peak with the closest RT. The setting cannot be used to specify that if no peak meets all criteria to report no peaks found.

    There is an Action available in the Tools menu that will zero a peak target if no qualifiers are found, but that will not zero peaks based on the qualifier outlier. It should be possible to write a script that would do what you want, but that could involve a fair amount of programming.

    One possible solution would be to utilize Compounds at-a-Glance view with outlier browsing. Select the outlier you want to review, in your case Qualifier Ratio, and then on the Outlier tab in Setup Layout specify to Show panes with outliers. This will produce a view of only the target peaks that have the qualifier ratio flagged.

    Then go to the Manual Integration tab, enable manual integration, and select all of the peaks that you would like to zero. You can use shift or ctrl left mouse click to select multiple samples/compounds and then use zero peak. This will set the target response and concentration to zero.

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