Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis

•Genomic and transcriptional analyses have paved the way to study Mycobacterium tuberculosis (Mtb) at a molecular level.•Shotgun-MS, S/MRM and DIA/SWATH-MS are different modalities that have been used for proteomic analyses of microbes.•DIA/SWATH-MS can consistently quantify ∼2700 proteins of Mtb over many samples and conditions.•DIA/SWATH-MS also supports the analysis of post translational modifications of bacterial pathogens.•The systematic proteomic analysis of sample cohorts describes aspects of the behavior of biological systems that are not apparent from genomic and transcriptomic analyses.

Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human host. Here we review omic studies in Mycobacterium tuberculosis, the causative agent of tuberculosis, with a particular focus on proteomic methods and their application to the bacilli. Likewise, the discussed methods are directly portable to other bacterial pathogens.