I need to quantify the total protein content from bacteria whole lysates. I've heard that Lowry assay is more sensitive in protein quantification, respect to Bradford assay due to the presence of membrane
The two assays are similar in sensitivity with respect to detecting protein (roughly 1 microgram). More sensitive fluorescence-based assays are available. If you are concerned about membrane material interfering with the assay, then you can either spin down the membranes in a centrifuge, or you can dissolve the membranes in detergent. You can still do the Lowry assay on detergent-containing samples, but not the Bradford assay.
Just a quick question - why do you not consider the micro-BCA methodology from Pierce (http://www.piercenet.com/product/micro-bca-protein-assay ) which works well for low concentration determination. It is also tolerant (to an extent) of detergents so will work (hopefully) well for work with membrane proteins.
Enea :) I would also go for the Bradford, but make sure to dilute your reference protein (ie, BSA) in the same buffer you will use to obtain your cell lysate. In fact, the detergents present in your lysis buffer may absorb differently as compared as the solvent you will use to dilute the BSA, and therefore alter the colorimetric assay outcome.