19Staphylococcus aureus is a major opportunistic pathogen that is exposed to antimicrobial 20 innate immune effectors and antibiotics that can disrupt its cell membrane. An 21 understanding of S. aureus lipid composition and its role in defending the cell against 22 validated the molecular characterization and showed the principal species present in each 33 strain were predominately anteiso-and iso-branched chain fatty acids. Though the fatty acid 34 and lipid profiles were similar between the S. aureus strains, this method was sufficiently 35 sensitive to distinguish minor differences in lipid composition. In conclusion, this nESI-36 MS/MS methodology can characterise the role of lipids in antimicrobial resistance, and may 37 even be applied to the rapid diagnosis of drug-resistant strains in the clinic. 38 3 39 101 102 6 103 Materials and methods 104 S. aureus culture and lipid extraction 105 All reagents and culture media were purchased from Sigma-Aldrich Ltd. S. aureus Newman 106 (methicillin-susceptible; MSSA), BB270 (methicillin-resistant; MRSA) and Mu50 (MRSA and 107 vancomycin intermediate-resistant) were sourced and cultured in Müller-Hinton broth as 108 described previously [22]. Briefly, each bacterial strain was prepared by inoculation of a 109 colony from an agar plate into 10 ml Müller-Hinton broth and cultured at 37°C with shaking 110 until reaching an OD 600nm = 1 (~1 × 10 9 colony-forming units [cfu]). Bacterial cells were 111 harvested (1000 × g, 10 min), washed in PBS before a repeat centrifugation and removal of 112 the supernatant. Lipids were extracted according to the Bligh-Dyer method [23], dried under 113 nitrogen, and stored at 4°C until analysis by mass spectrometry. 114 115 157