Highly selective detection, rapid response (<20 s), and superior sensitivity (R-air/R-gas > 50) against specific target gases, particularly at the 1 ppm level, still remain considerable challenges in gas sensor applications. We propose a rational design and facile synthesis concept for achieving exceptionally sensitive and selective detection of trace target biomarkers in exhaled human breath using a protein nanocage templating route for sensitizing electrospun nanofibers (NFs). The mesoporous WO3 NFs, functionalized with well-dispersed nanoscale Pt, Pd, and Rh catalytic nanoparticles (NPs), exhibit excellent sensing performance, even at parts per billion level concentrations of gases in a humid atmosphere. Functionalized WO3 NFs with nanoscale catalysts are demonstrated to show great promise for the reliable diagnosis of diseases.