We improved the measurement capabilities of PTR-MS for real-time monitoring of breath VOCs in the clinical environment. In the first study, we evaluated the effects of a modular ion-funnel onto PTR-MS performances in terms of sensitivity and LODs. In the second study we optimized instrumental conditions for direct breath-resolved real-time monitoring of highly reactive compounds. In the third study, we evaluated the effects of potential confounders from the clinical environment such as elevated inspired O2 concentrations onto PTR-MS based VOC analysis.<eng>