Find Retention Time of Analyte?

[moreysalzman]

Hey all,

I work at a toxicology lab, and I'm trying to learn methods. I'm trying to move a method from one LCMS to another, but its a completely different LCMS (other than the column) hence the RT should be a little different.

Hope this is not a naive question:

How exactly can I find the retention time of an analyte? Is there a specific scan mode to use? Like a readout that has relative abundance vs retention time. Something that I could just have scan over 5 min and see the main peak.

The MS is a Thermofisher Quantiva (it's nice ), and im mostly using Xcalibur for the software
I'm happy to give more info if necessary.
Thanks in advance

[lmh]

If you run the same gradient with the same column and same solvents on a different system, you should get approximately the same chromatogram, but slid to the left or right according to the dead volume of the system ("should" but I won't swear you always will!). If you run different solvents then obviously things may change substantially.

Hopefully if you change MS instrument the ion you're looking for should remain the same too, but it doesn't always. You may find that a target analyte that always ran as a hydrogen adduct on one system mysteriously runs as a sodium adduct on another. Obviously if you're moving from a ToF or single quad instrument to a triple, you will also need to know what mass transitions are best on the triple.

The usual approach I'd use is:
(1) For a triple, get the standard, and use infusion mode (i.e. teeing of a steady flow of dilute standard into a flow of solvent from the LC, combined into the MS) to find the correct mass transitions.
(2) Then run the chromatography method that I know works from another system, and expect my peak of with the expected MRM transitions within a minute or so of where it normally happens. This approach only needs to run the MRM events.

The less-happy approach where I have no standard:
(1) For a triple, include a full scan event as well as any MRMs that I expect to work, if I have a preconception of how the compound will fragment. Run the positive control sample, where I know I see a peak in another system, and look for appropriate parent ion masses in the vicinity of the correct retention time.
(2) Run daughter ion scans of the appropriate parent ion, at a couple of different collision energies, using my positive control sample, to find sensible fragments and corresponding collision energies.

[moreysalzman]

Thank you lmh, this will give me a better starting point!

And thank you for the insight into how the RT could change (or from what youre saying, shouldnt change much) by switching instruments. Its probably something else other than RT thats wrong with my method.

Update: I was able to figure this out a while back, and indeed, opening the RT window to the full length of the scan and then looking at the scan filters for each transition is how I found retention times.