I am trying to check for some proteins if they are located in the inner or outer mitochondria membrane after treating the cells with a neurotoxin. I am using PK to digest the mitochondria, but I didn't find a protocol regarding separating the soluble from insoluble fraction after PK digestion. I tried to centrifuge the sample after stopping PK digestion for 14K rpm for 10 min, but I didn't get any positive results for the markers from the soluble fraction in western blot.
Thanks