A simplified method for comprehensive capture of the Staphylococcus aureus proteome: S. aureus proteome data table

Staphylococcus aureus is a major human pathogen causing myriad infections
in both community and healthcare settings. Although well studied, a
comprehensive exploration of its dynamic and adaptive proteome is still
somewhat lacking. Herein, we employed streamlined liquid- and gas-phase
fractionation with PASEF analysis on a TIMS-TOF instrument to expand
coverage and explore the S. aureus dark proteome. In so doing, we captured
the most comprehensive S. aureus proteome to date, totaling 2,231 proteins
(85.6% coverage), using a significantly simplified process that
demonstrated high reproducibility with minimal input material. We then
showcase application of this library for differential expression profiling
by investigating temporal dynamics of the S. aureus proteome. This
revealed alterations in metabolic processes, ATP production, RNA
processing, and stress-response proteins as cultures progressed to
stationary growth. Notably, a significant portion of the library (94%) and
proteome (80.5%) was identified by this single-shot, DIA-based analysis.
Overall, our study shines new light on the unexplored S. aureus proteome,
generating a valuable new resource to facilitate further study of this
dangerous pathogen.