| | Re: phospho to total protein
I understand that the ratio gives you a percentage of activated protein, and that phosphatases will affect the absolute amount of phosphoprotein at a given time. However, phosphatase effects are still present in the ratio (since you are just measuring the same thing but dividing by total proteins). To me, it seems like you are getting the same amount of information, unless the total levels of phosphoprotein changes upon your perturbation.
I am still not satisfied explanations given thus far, aside from "it is the standard in the field". I mean it is really a simple question.