This work package (WP3) focuses on clinical application through dose reconstruction and adaptive proton therapy (PT) by utilizing realistic treatment plans for representative cancer cases such as brain, lung, breast, and prostate tumors. By combining state-of-the-art clinical software with Monte Carlo simulations, the project generates diagnosis-specific models and software capable of triggering real-time adaptive protocols based on dose thresholds translated from the CoDA signal. A key innovation includes addressing radioresistance by simulating oxygen depletion (hypoxia) levels through prompt gamma (PG) spectra, enabling real-time dose adaptation to tumor tissue resistance. Furthermore, the system explores advanced tumor-tracking capabilities by characterizing characteristic PG emissions, ultimately aiming to integrate the NOVO concept into clinical adaptive therapy workflows.