This question comes up a lot and, while I have my own general rule that I picked up from a talk by someone way smarter than me, I wasn't aware of this paper till I stumbled upon it (while looking for something completely different...) where they try to answer this very question!
It is worth keeping in mind that this paper was submitted in 2013 and we've learned some stuff since then, but this is a really thorough approach to the topic, comparing LFQ and two isobaric tagging technologies on a fully characterized dataset.
There is a lot of good info on the paper -- from analysis of 2D separation for reporter ion experiments, to the LOD/LOQ of said experiments on the instrument platform they utilized in the study. In the abstract they even provide a single summary of the maximum percentage of coisolation interference they recommend using (which is lower than what I use), but the logic for why they use it is much better than what I had!
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