The noninvasive method of breath gas analysis is widely used in human studies to explore the diagnostic potential of endogenous VOCs [1]. Proton transfer reaction mass spectrometry (PTR-MS) measures a wide spectrum of VOCs online, fast and nearly simultaneously from ppm (part-per-million) down to ppt (part-per-trillion) levels [2]. In the German Mouse Clinic (GMC) mutant mouse models for human diseases are comprehensively phenotyped to better understand the underlying molecular mechanisms and to develop new therapeutic strategies. Despite the advances in PTR-MS instrumentation the exploration of exhaled VOCs of small animals is still challenging and, hence, rather uncommon and furthermore restricted to specific VOCs as acetone or ethanol [3, 4]. Therefore, the aim of our study was to develop a PTR-MS setup suitable for unrestrained screening of exhaled VOCs in mouse models of human disease.