I am testing the expression of a bacterial protein in the context of the infection. I have a human cells infected with bacteria and I would like to check in which time point the expression starts/increases. I am afraid that there are so many human protein compare to the bacteria that, unless my protein of interest is highly express, I won't be able to detect it with WB. In parallel, I am doing LC-MS/MS to see if this technique would be better but again I am limited by how much protein I can load, which I am afraid 99% will be human.

Does anyone had experienced this, to know if my suspicious are right or wrong?

Thank you.