The current state of microbial proteomics: where we are and where we want to go.

Proteomics allows the assessment of cellular processes in an unprecedented scale by providing a comprehensive quantitative and qualitative overview of the protein content of a cell. Consequently, proteomics has been employed to investigate a multitude of bacterial processes ranging from the analysis of environmental communities, identification of virulence factors to the proteome-guided optimization of production strains. Proteomics has, in short, become an indispensable tool for the global analysis of bacterial physiology. Nonetheless, challenges exist, especially in the accurate prediction of phenotypic consequences based on any given proteome composition. In this review, we will give an overview of current highlights in the area of microbial proteomics, discuss some current challenges and present new developments that may help in overcoming them.