Mass Spectrometry-Based Proteomics of Microorganisms

Proteomics is a growing field which aims to study the structure, function, and interactions of proteins. Mass spectrometry has become a powerful tool in the study of proteins due to the distinct masses of the different amino acids that compose proteins. In this work, we use a bottom-up proteomic approach to characterize protein expression in microorganisms. We focus on two organisms of interest: the mycobacteriophage CrimD and the bacterium Helicobacter pylori. The infection of Mycobacterium smegmatis by CrimD was frozen at three different time points with the goal of characterizing the infection process and identifying the roles of unknown proteins found in the genome. In H. pylori, the regulatory protein ArsR was purified in order to investigate the potential of post-translational modifications similar to those in closely related organisms. In our analysis we use reverse-phase high performance liquid chromatography coupled to a linear ion trap mass spectrometer with an electrospray ionization. These techniques have yielded reproducible results. The CrimD infections yielded high confidence protein results, while the H. pylori samples show low confidence identification of the modifications of interest.