Differential Protein Expression in Bacteriophages CrimD and Larva

Proteomics studies allow us to answer questions about differential protein expression across different systems. Mass spectrometry is a powerful tool in these studies due to the distinct masses of the amino acids that compose proteins. In our experiment, we used a bottom-up approach and focused on two bacteriophages found on the William & Mary campus, CrimD and Larva. The infection of Mycobacterium smegmatis, a nonpathogenic model for tuberculosis, by these two bacteriophages was frozen at five different timepoints, and our goal was to compare the differential protein expression across the samples in order to gain a greater understanding of the proteins of unknown function expressed by the phages. In our analysis, we used reverse phase liquid chromatography coupled with 2D and 3D ion trap mass spectrometers fitted with a nanospray ionization source and an electrospray ionization source respectively. Protein expression was determined using the Proteome Discoverer software. These techniques had been previously used in our lab with a focus on phage T7 and CrimD, and reproducibility of data became a priority. Specifically, the pulling and packing procedure for the chromatography columns as well as the instrument methods governing each sample run required significant optimization, especially after a mid-year switch in instrumentation