A Simple Method to Isolate and Characterize a Bacterial Outer Membrane Proteome by Bottom-Up Mass Spectrometry

The outer membrane of gram-negative bacteria plays a critical role in protecting the cell against external stressors, including antibiotics. Given its importance to the resistance mechanisms, the outer membrane is a prime target for antimicrobial drug discovery. To facilitate discovery efforts, however, a precise characterization of the outer membrane protein content – or the "outer membrane proteome" - and possible variations during bacterial resistance, is important. This information is necessary to understand how bacteria interact with their host organism during infection. However, proteomic-based investigations of the bacterial outer membrane remain technically challenging, given this cell compartment's lower abundance and high hydrophobicity. We report here a simple but efficacious enrichment of the bacterial outer membrane proteome for downstream characterization by mass spectrometry. We start with a dual detergent approach to preferentially solubilize the outer membrane, followed by reconstitution in peptidisc library to isolate and purify the entire outer membrane proteome at once. Our method identifies 71 outer membrane proteins (OMPs), including 26 integral -barrels and 26 lipoproteins; many of which are present with high-intensity and peptide number values, indicative of a high abundance in the library sample. Given this enrichment, the method may be useful for comparing outer membrane proteomes. We also show that the library can also be employed for downstream protein binding assays.