In high-resolution tandem mass spectrometry such as Q-Exactive Orbitrap and Q-TOF, full scan/ddMS2 is commonly used. In this mode, a full scan is first acquired, followed by fragmentation of top N ions to get MS/MS spectra. The selection of top N ions is completed by quadrupole in this case. However, quadrupole is a low-resolution mass filter with mass error of 0.5 Da, how does the quadrupole differentiate ions with accurate mass differences smaller than 0.5 Da? For example, if two different ions with accurate m/z 319.1300 and 319.2600 are both top N ions, will the quadrupole consider them the same ion, and send them together to the collision cell for fragmentation instead of one by one in the case of 319.1300 and 419.1300? Thanks.
Due to the resolution limit of the quadrupole, both ions (m/z 319.1300 and 319.2600) will pass through it to the collision cell. If the isolation window is set to be wide, ions even a few Da apart could pass through the quadrupole. If both ions (m/z 319.1300 and 319.2600) meet all the selection criteria, both will be fragmented with the precursor ion setting at m/z 319.1300 and again at m/z 319.2600 even their m/z values are essentially the same for the quadrupole, although there is no real need to acquire basically the same data twice. Of course, different systems may handle things differently.
Lei, sorry for the confusion. I hope the revision to my original post above helps. The bottom line is that individual product ion spectrum for one of the precursor ions cannot be acquired without the interference from the other if the quadrupole cannot resolve the two co-eluting ions.
In this case, you will have MS MS data for both ions (the quad send both ions in the same scan). Both Q TOF and Q Exactive can not provide such selectivity on their quad. Even on Orbitrap Fusion Lumos it would not be possible to acquire accurate mass fragmentation (by definition of 5ppm mass deviation) for small molecule. In case of top N approach, even if the ion 319.2600 does not belong to the top N ions, it will still be selected together with the ion 319.1300, of course with much smaller contribution to the acquired MS MS spectrum.
I agree, things cannot solved by mass spectrometric resolution. On the Q-Tof You might use alternating enegies (MSE) to find out if there are ionization conditions that suppress one of the two investigated compounds. They might be different in ion mobility if this approach is available. And maybe they can separated by HPLC....
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