Dear Yang,
Thank you for your inquiry.
We have not had issues with lysis with the specific cells and Lysis buffer that we tested this on. We have tried other Lysis buffers though, and they have worked to certain extents (some better than others).
What cell line or primary cells do you use? I think that it is worth trying in parallel a few lysis buffers, as some work better for some cells than others.
Also, I wanted to ask - what do you mean by difficult to lyse them - so there is no clear difference between the pellet and the supernatant? Is the protein concentration in the supernatant very low?
Hope this is helpful and please let me know if I can do anything else to help.
Anca