My protein of interest is around 70 KD and I have seen there is another isoform at 100 kD. When I do western I can see both the 70 and 100 kd band. However, in my Immunprecipitation I could never see the 100 KD band , only the 70 KD band pulls down with my IP. This I have seen more than 20 times , so its reproducible.
I was wondering, what might be the possible explanation for it. Why the 100 KD disappears in IP ? any good scientific explanation will be highly appreciated.