If you are doing MS3 based reporter ion quantification, you should really check out MS3-IDQ!
The paper is available here.
The idea is really simple. If you are going to be getting both MS2 and MS3 based data on your peptide, you might as well utilize it to increase your identification and localization rates, right!??
I'm sure this isn't the first group to have thought about it -- but implementing it? Umm....yeah..... There are a ton of factors to consider from the instrument side and from the data processing perspective. I, for one, am really glad that they did the work so I don't have to!
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