Difference in retention time of the quantifier and qualifier

Discussions about GC-MS, LC-MS, LC-FTIR, and other "coupled" analytical techniques.

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Hello!
I am working with an HPLC-MS/MS instrument to detect disinfectants from in different matrices (eg. wastewater, sludge, soil) and routinely measure the quantifier and one qualifier for my analysis. Since I work with matrix-rich samples, there are frequently noise peaks especially at low concentrations (even after SPE cleanup). Therefore, I am often not sure which peaks to integrate as my qualifier. Should the quantifier and qualifier always co-elute at (nearly) exactly the same retention time, or is it possible that their RTs differ, eg. by 20 seconds?

I would assume quantifier and qualifier should usually co-elute simultaneously as the fragmentation takes place in the MS and not on the LC column? Or are there other processes that could affect the retention time of the individual fragments?

Your help is much appreciated!
If the scan time for each MRM is less than 20 seconds (should be less than 1 second I would imagine) then the two should co-elute if they come from the same analyte. The column should not separate the masses, it should deliver the analyte whole to the source which then charges the analyte, which is then brought into the entrance of the MS where it is then broken into mass fragments. Therefore they should always maximize an the same retention time, within a window corresponding to the scan rate of the MS, which should have the peaks maximizing within a second of each other.
The past is there to guide us into the future, not to dwell in.
Yes, they should coelute. My strategy is to determine a whole selection of potential mass transitions, and then run a real sample to find out which work best. Ideally you'd like to use the most intense mass transition as your quantifier, but if it's not very selective, and there are adjacent, badly-resolved peaks next to the peak that you know is correct from running a clean standard, then it will be hard to integrate reliably. The same goes for qualifiers. If the qualifier ion isn't very selective, it's not giving you much assurance that the peak is the right thing, and if it's prone to picking up other nearby chemicals, then there's a risk of rejecting genuine peaks for having a bad ratio, because the ratio has been contaminated by something.
So typically, I set up 5 mass transitions if I can, and then select two that are reasonably intense and reasonably clean as the quantifier and qualifier.
In "real" samples, selectivity is often worse than it ought to be by pure chance, because the sample is likely to contain things that are closely related to your analyte, either as real components, or as breakdown products of real components.
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