To establish general differences between the protein expression in S. aureus strains, five methicillin sensitive S. aureus (MSSA) strains and five methicillin resistant S. aureus (MRSA) strains were compared both individually and as MSSA and MRSA groups in the absence of antibiotics. Proteins were compared by ultra-performance liquid chromatography-mass spectrometry. Sample Processing Protocol A whole protein extract was obtained from each strain using a modified Bligh and Dyer method. This protein extract was then digested using trypsin and the the Waters RapidGest SF Surfactant Procedure. The digested protein sample was then analyzed by UPLC-MS using a Waters nanoAcquity UPLC sample manager fitted with a binary solvent manager. Mass spectrometric detection was conducted using a Waters Synapt G2-Si. Data Processing Protocol Proteins were identified using Progenesis QIP and the Uniprot S. aureus database. The following search conditions were used. The allowed maximum missed cleavages = 1, the allowed false discovery rate = 4% and the maximum protein size was set to 250 kDa. Peptide modifications were set to variable and included carbamidomethyl C, deamidation N, deamidation Q, oxidation M and propionamide C. The ion matching requirements were fragments/peptide of 1 or more, fragments/protein of 3 or more and peptides/protein of 1 or more.