According to some embodiments, a method can identify and discriminate contributions from one or more noise sources using the multi-level structure of a quantum system with three or more levels. The method can include: preparing the quantum system in a predetermined state; applying one or more control signals to the quantum system; measuring values of one or more observables of the quantum system that quantify the quantum system's response to the noise sources and the one or more applied control signals; extracting noise spectra information associated with the noise sources from the measured values; and identifying contributions from the one or more noise sources based on the noise spectra information.