I am looking to see if various proteins of interest are mis-glycosylated, and trapped in the ER or Golgi apparatus. Initially, my experiments have been focussed on performing western blots to look for bands running at different molecular weights (i.e. no glycosylation = lower MW); the lysis buffer I am using is 10mM NaCl with 1% Triton-X100 in Tris.

My concern is that I am missing the real glycosylation state of the protein because I am not lysing the whole of the cell, and that the compartments where my mis-processed protein is found are never actually going into the lysate.

If anyone has any suggestions as to ideal conditions to look for defects in glycosylation in endogenous proteins from in vivo samples, I would be very grateful.

Thanks in advance.