Staphylococcus aureus is a prominent bacterial pathogen responsible for an array of human diseases in both hospital and community settings, which underpins a huge financial burden worldwide. Emergence of methicillin resistant strains (MRSA) initially in hospitals (HA MRSA) and later in community (CA MRSA) has added more challenges both therapeutically and financially. Knowledge of the pathogenesis and virulence factors of this bacterial pathogen remains incomplete despite intense research and alarmingly, the distinction between HA MRSA and CA MRSA is becoming blurred due to replacement of hospital clones by dominant and more virulent CA MRSA. We investigated the differential proteomics of four clinical MRSA strains (two HA MRSA and two CA MRSA) in three biological replicates, in vitro at stationary (OD₆₀₀=1) and log (OD₆₀₀=0.4) growth phases using a novel proteomic approach. Proteins were extracted using an optimized extraction protocol coupled with FASP digestion. Mass spectrometric data acquisition was performed in both data-independent and data-dependent methods using a TripleTOF 5600+. Using the raw data from data-dependent acquisition, a protein database was constructed using the Paragon algorithm to acquire peptide-spectrum matches. This database was then used to extract quantitative information from raw data-independent mass spectrometry files. Multi-strain protein clustering by sequence identity was determined. Quantitative peptide information was assigned to protein clusters, normalised and analysed for significant abundance differences. Protein clusters with differential abundance is used to interpret the functional characteristics of the significant proteins of interest. This study has revealed unique protein profiles for each of the clinical strains and provides important information for delineating the molecular pathogenesis of HA MRSA Vs CA MRSA.