We all know "What is immunoprecipitation?" and we do it very frequently.
But when we get the results come from WB or MS/MS we saw many interacting proteins (both direct and indirect). [No need to say about proper set of controls].
Now the catch is to understand if the Interactions that we get are of biological or biochemical...!!! (I hope you get it).
Because, according to protocol we put the cell lysates on antibody (bound/unbound to beads) and keep it for 1-2 hours. Now, the point is within this incubation period we may loose some biological interactions and get some biochemical interactions (because of IP-buffer). Then how can we be sure that the interactions are because of the cellular signals...???
I know there can be a big debate...!!! But I want your views and prospects of looking at it. That will help me as well as many researchers to understand the biology and the methods of detection.
Thanks.
Hoping for answers..!!
My VIEW!!
I accept all the possibilities that you mentioned during the immuno-precipitation and it might not help to directly infer that the interactions are because of cellular signals. But a positive hit in the experiment gives me a prospective candidate to look upon to, in vivo or cell-lines. So i see it as a "GOOD start technique" which would ease my pain of mapping PPIN and help me for looking into the possibilities whether the interaction are or are not due to the cellular signals.
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