Abstract Instabilities in turbomachinery operation originate from intrinsic flow unsteadiness, sudden variations of operating conditions, and interactions with the surrounding system, affecting both system stability and machine reliability. The flow unsteadiness, presenting a characteristic behaviour, requires a deep understanding of the underlying flow fundamentals, a careful analysis using advanced experimental methods and a clear distinction on how the system might lead to instabilities. The identified approach addresses deep surge and second quadrant characterization. The analysis presented here benefits from the responsiveness and flexibility of the experimental test rig, fine tuning of the system layout, the instrumentation installation, and the transient tests procedure. The main focus area is the time-frequency analysis of flow and pressure signals at transients, thus providing a proper reconstruction of flow mechanisms and instability evolution. Valuable techniques include: short-time fast Fourier transform, wavelet analysis, and Wigner-Ville distribution; coherence between flow and pressure, to trace waves propagation, is considered too. These, presented outlining their strengths and weaknesses, are evaluated considering real time field applicability with regards to computational resources too. The experimental campaigns and data processing are presented, with a test matrix covering a wide range of parameters, including system layout and surge volume size, rotational speeds, flow rates ranging from nominal point to full second quadrant operation. These data are vital for system modeling validation for a full compressor-system digital twin. Results indicate the importance of ensuring reliable data acquisition and analysis, with adequate instrumentation range, accuracy, synchronization, responsiveness and positioning.