Abstract

Phages, as viruses that specifically target and eliminate bacteria, present as a promising treatment strategy against antibiotic-resistant bacteria. Giant phages, however, with longer genomes and a higher level of virion complexity, remain understudied. This research aims to evaluate the applicability of data-dependent acquisition mass spectrometry (DDA-MS) versus data-independent acquisition mass spectrometry (DIA-MS) to characterize and quantify the copy numbers of virion proteins of the giant Salmonella phage SPN3US.  Accurate copy number estimations require confirmation of protein sequences in the mature virion, as previous analyses showed nine SPN3US head proteins were shorter than their predicted lengths, as they had been cleaved by a phage protease gp245. This study identified 16 cleavage sites in 10 head proteins, including a new substrate gp94, ensuring correct use of virion protein sequences and their molecular weights for copy number estimations. Virion proteins with known copy numbers were used to adjust mass spectral data to estimate the copy number of individual virion proteins. Analysis of these estimations showed that DIA-MS provided significantly more credible copy number estimations than those obtained using DDA-MS. Overall, the data demonstrated that mass spectrometry (MS) is a promising method for characterization and quantification of the highly complex giant SPN3US virion particle. This work provides the foundation for future studies on giant phage and suggests potential applications of MS for copy number estimations of other tailed phages.

Publication Date

12-15-2025

Document Type

Thesis

Student Type

Graduate

Degree Name

Bioinformatics (MS)

College

College of Science

Advisor

Julie A. Thomas

Advisor/Committee Member

Eli Borrego

Advisor/Committee Member

Stefan Schulze

Comments

This thesis has been embargoed. The full-text will be available on or around 12/21/2026.

Campus

RIT – Main Campus

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