you can break cells with detergents (eg sds, triton) or sonication or with a homogenizer (or a combination).
if you want to separate by size then you can run sds-page. if by charge and size then native page or urea page. if by pI then ief page. and the appropriate apparatus and power supply.
Thanks, I think I will try to separate them in both ways, by size and then by charge.
Sorry I am novice and I have some questions please:
What do you mean by 'pl'?
Can I run the electrophoresis without breaking the cell membranes? Will it work?
Do I need to have a medium to apply the electric field? I.e. do I need to put the cells in a material and then apply electric field?
Is there a way to use a probe to apply the electric field on a specific point, rather than the whole thing?