MassHunter Qualifier Ion Not Found


We have been having issues with MassHunter Quant Software (version 12.0) randomly not finding qualifier peaks (284.1 -> 256.0). The TIC shows that the ion is there and was extracted (see screenshot, right-most panel), and when we open up the data files in the Qualitative software the peak is found at the indicated RT (see screenshot, highlighted peak). We have tried re-building the method from scratch to no avail. Of note, when we analyze the data in an older version of MassHunter Quant it integrates the peak just fine. All of the integration and quant method parameters are identical.

Quant View

Qual View

  • I've narrowed down the issue: the compound names in the acquisition method scan segments are off by a space for the quantifier ion and qualifier ion (7 amino vs. 7amino). However, the precursor ions are the same and I have never had this issue when applying this quant method to other batches that were acquired with the same spelling discrepancy. Still unsure how to resolve this, it won't let me update the compound name in the quant method, and if I manually add the qualifier transitions it says "no data points" because the name doesn't match up (even though the ions do).

    Has anyone else had this issue?

  • Hello  ,

    Just to share with the Community what we discussed in your call to support, what you are observing is generally the expected behavior in quant.

    If a compound name in your quant method exactly matches a compound name in the acquisition method, then quant will ONLY allow extraction of the signals that are associated with that compound name in acq. This is to help with verifying that the selected signals are all for the same compound.

    This behavior can be dependent on the version of acquisition used to acquire the data and the version of quant used to process the data. It is possible that one version of quant will be able to process a set of data that contains a typo in the acquisition compound names without issue, but another version will not allow the loading of data for the signal name that does not match.

    Fixing the compound name in acquisition will resolve the issue in future batches. For data already acquired with mismatched compound names, you can change the name of the compound in quant so that it doesn't match any compound name in acquisition. Then you should be able to extract and use any signals for that compound. You can add a space to the end of the compound name in quant and that should be enough to break the link.

    In general, it is recommended to utilize this matching feature and make certain the acq and quant compound names match to avoid the extraction of ambiguous signals. 

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