The bags were then placed in an incubator at 37 °C for 50 h. After 50 h, the headspace was analysed using selected ion flow tube mass spectrometry (SIFT-MS) and thermal desorption – gas chromatography – mass spectrometry (TD-GC-MS) as described later. Mycobacterium smegmatis was not analysed by mass spectrometry. SIFT-MS has been described in detail previously (Spanel & Smith, 2011). It is a real-time trace gas and VOC analyser especially useful when looking at low molecular mass compounds; it is also better at obtaining quantitative data than GC-MS as the headspace

is analysed directly. Analysis requires the generation of precursor ions which are produced in a microwave discharge and are selected by the first of two quadrupole mass filters before being injected mTOR inhibitor into a fast flowing helium carrier gas. These ions then react with the VOCs in the sample which is drawn into the flow tube via a heated capillary. The available precursor ion species are H3O+, NO+ and O2+. The

precursor and product ions buy Nivolumab in the carrier gas are sampled by a downstream orifice and pass into a differentially pumped second quadrupole mass spectrometer and ion counting system for the analysis. A PDZ-Europa Mk 2 instrument was used in this study. Full spectra of the count rates at each m/z value were recorded for all the samples using each precursor ion. The identities and concentrations of various components were determined using an on-line database containing reaction rate coefficients (Smith & Spanel, 2005). The Nalophan bags were connected to a thermal desorption (TD) tube for subsequent analysis by GC-MS to preconcentrate the headspace via an automated pump using 500 mL of BCG headspace gas. Standard stainless steel sorbent cartridges were used, containing dual packing comprising 50% Tenax TA and 50% Carbotrap (Markes International Limited, Llantrisant, UK). Cartridges were conditioned before use by purging with helium carrier gas for 2 min at room temperature Org 27569 followed by 1 h at 320 °C. Captured volatiles were analysed using an

AutoSystem XL gas chromatograph equipped with an ATD 400 thermal desorption system and TurboMass mass spectrometer (Perkin Elmer, Wellesley, MA). CP grade helium (BOC) was used as the carrier gas throughout, after passing through a combined trap for the removal of hydrocarbons, oxygen and water vapour. Cartridges were desorbed by purging for 2 min at ambient temperature and then for 5 min at 300 °C. Volatiles purged from the cartridge were captured on a cold trap which was initially maintained at −30 °C. Once desorption of the cartridge was complete, the trap was heated to 320 °C using the fastest available heating rate and maintained at that temperature for 5 min whilst the effluent was transferred to the gas chromatograph via a heated (180 °C) transfer line coupled directly to the chromatographic column.