Mass Spectrometry-Based Analysis of Surface Proteins in Staphylococcus aureus Clinical Strains: Identification of Promising k‑mer Targets for Diagnostics

Surface proteins of Gram-positive bacteria are critical
for adherence
to host tissues, evasion of the immune system, and interaction with
the environment. They can be utilized as biomarkers in diagnostics,
for vaccine development, and as therapeutic targets due to their accessibility
and role in pathogenicity. If utilized as diagnostic targets, surface
biomarkers should be highly conserved across different strains of
the pathogen, unique to the species to avoid cross-reactivity, abundantly
expressed on the bacterial surface, and accessible to antibodies or
detection reagents. Mass spectrometry-based proteomics methods have
advanced the studies of surface proteins, often in combination with
selective enrichment strategies such as tryptic “shaving”.
In this study, 11 clinical strains of Staphylococcus
aureus underwent tryptic shaving to identify common
surface proteins. Further bioinformatics analysis confirmed that these
proteins are encoded in the core genome of S. aureus strains and contain species-specific peptides. In silico analysis
identified 26 k-mer peptides in 15 surface proteins with structural
accessibility to detection agents, making them the ideal targets for
molecular diagnostics or as linear epitope targets for vaccine development
or therapeutics. Among the identified candidates were known virulence-associated
proteins such as PbpA, Sbi, and Asp23previously studied in
the context of vaccinesas well as uncharacterized proteins
encoded by the gene loci SAUSA300_1904 and SAUSA300_1685, whose unique
and surface-exposed features suggest unexplored diagnostic potential.