Chromatography Forum

I'm trying to understand Tandem MS better. I ran into some examples which I don't fully understand. Here is what I see in Mnova for Waters MRM injection:

I don't understand why it shows as 3 different detectors. Judging from Retention Times they start one after another, but they overlap and show different data. And they measure different sets of ions. I mean, in reality we have the same quadrupoles switching between one set of ions and the other, right?

Also, in the Waters RAW files each channel comes with 2 pairs of ions - I assume precursors (bigger mass) and products (smaller mass): For some reason Mnova shows the bigger masses in spectra - is this expected? When doing SRM/MRM do you switch between "show me precursors" and "show me products" in spectra?

I'm only used to viewing data in MassLynx, which is Waters' software. This would have presented things a little more intuitively.
I assume these data were collected by a tandem quadrupole instrument in MassLynx. If so, behind the scenes, there would be a number of what Waters call "functions", each corresponding to a different chemical, and each collecting a number of mass transitions, which Waters call "channels". MassLynx will present a "TIC" for each function, i.e. a total chromatogram summed from all transitions that it collected for that function (= chemical; it's really confusing if you have multiple chemicals in one function, though it can be done). This isn't a real TIC, and Waters, too, report the mass of the precursor if you turn on "base peak" as a notation on the chromatogram. However, double-clicking the peak should show the MS2 spectrum, though it's not a real spectrum as it's composed only of the ions the instrument happened to be collecting. I very rarely bother with spectral views when I've collected MRM data as they're grossly misleading. Chromatograms are the way to go!

I am guessing that the TIC's you're seeing in Mnova correspond to the TIC's of each function in MassLynx. It is quite normal that they have different time-ranges. Usually you would set up each function so that it starts collecting the relevant transitions just before the peak normally elutes, and stop just after, so the instrument isn't collecting data unnecessarily. The more transitions it has to do simultaneously, the shorter the time it can dedicate to each, so the lower the sensitivity, so you often aim to collect transitions only when needed.

I think I got it: Waters groups multiple m/z (channels) in a function and switches between these channels at some rate. It also may switch between functions if those functions span the same time range. E.g. if we set up:Then first 2 minutes it would switch between 3 masses (100, 200, 400). Then after 2 mins it will start collecting only 300 and 500 m/z.

It's interesting that Waters turns them into multiple functions. Opposed to that when dealing with SIM (which to me is the analogy of SRM/MRM in Tandem MS) in ChemStation, we can set up collecting different m/z at different time e.g. And this will end up being a single chromatogram. Though I think these time ranges can't overlap.

I'm only used to viewing data in MassLynx, which is Waters' software. This would have presented things a little more intuitively.

You mention that it Waters this looks better - what's different there?

MassLynx labels the TICs with what they are. So it will tell you that the TIC is that for caffeine, or whatever.
I think Waters' philosophy is that the instrument is intended to be selective, selecting single chemicals, so you will want to see a chromatogram for each chemical, not a sort of sum-of-all-chemicals.
Note also that functions can overlap. You could collect transitions 200>154 and 200>131 for chemical 1 from 1 to 3 minutes; transition 300>213 for chemical 2 from 2 to 4 minutes, and another set of transitions for chemical 3 from 2.8 to 5 minutes, and the instrument will seamlessly sort itself out, dividing its time optimally between all the different transitions it has to collect at each point along the chromatogram.