To isolate membrane-associated proteins, which play diverse structural, catalytic, and regulatory roles in cells, they are often initially solubilized in detergents. Although detergents are essential for purifying membrane proteins, they tend to interfere strongly with subsequent analyses. A microfluidic method is presented here that surmounts this problem, allowing well-resolved mass spectra of test membrane-associated polypeptides, and their complexes with ions and detergents, to be acquired. As a front-end module it allows access to other advanced mass spectrometric strategies to be utilized toward defining biomolecular interactions. This opens up a new avenue for studying complexation and analysis of membrane proteins of general importance.