This white paper covers the challenges in debugging mixed-domain embedded systems in both the frequency and time domains. An overview on frequency domain analysis techniques and Fast Fourier Transform (FFT) basics is provided. Time gating is presented as a powerful tool that allows the correlation between the time and frequency domain. In addition we introduce a frequency domain mask capability that allows the oscilloscope to trigger on elusive events that occur infrequently in the frequency domain. Finally, we present a case study example that uses each of the discussed topics to help debug a problem in an actual embedded system.