Current methodologies for proteomics of bacterial surface‐exposed and cell envelope proteins

Abstract The study of surface‐exposed proteins has received increasing attention following the advent of genomic sequencing, which in turn has enabled predictive tools and facilitated the technologies for their analysis by proteomics. The exterior topology of a bacterial pathogen is the interface between the cell and environment and thus is the initial mediator for infection, providing an important reservoir for components that may be used for novel vaccine development as well as the characterization of new drug targets. The study of such biological molecules has however, been under‐represented in proteomics studies due to the difficulty involved in their analysis. Cell‐envelope proteins in bacteria are typically difficult to characterize due to their low abundance, poor solubility, and the problematic isolation of pure surface fractions with only minimal contamination. Here, we describe different cell envelope preparations for proteomic characterization, focused principally on gel‐free technologies. Fractionation techniques popularly used in proteomics are also explained with emphasis on surface and membrane‐derived proteins/peptides. Conditional confirmation of localization is also explored with emphasis on different prediction algorithms as well as on analyses of surface peptide fractions by the use of different search programs and their implications for the unambiguous identification of surface‐exposed and membrane‐embedded proteins. Finally, different quantification techniques are discussed that are important for the validation of identifications and for highlighting novel proteins that may warrant further study by independent techniques.