PNNL

Abstract

Mass spectrometry-based proteomics is a powerful tool for the detection and characterization of microbes of forensic and national security concern. Both targeted and untargeted proteomics methods have been developed for the taxonomic classification of unknown microbial samples. Targeted proteomics assays are can be designed for specific microbes of security concern. Untargeted, library-based matrix-assisted laser desorption-ionization time of flight (MALDI-TOF) mass spectrometry is now extensively used in the medical field for microbial identification. Several research groups have developed data analysis pipelines for organism identification/taxonomic classification from untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) data, an application which has some overlap with the field of metaproteomics. This chapter reviews these organism identification techniques. However, organism identification/classification is also commonly done by whole genome sequencing. Using examples from published literature, this chapter also highlights several examples of how proteomics approaches can provide information that cannot be acquired from DNA sequencing alone, such as distinguishing laboratory-adapted bacteria from closely-related wild isolates, and characterizing the growth medium of bacteria and the host cells of virus particles.