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The theoretical basis and practical peculiarities of a new integrated signal analysis method called as the system spectral analysis are considered. Using the simple analytical models of ultra-wideband signals in time domain, the possibilities, advantages and disadvantages of the system spectral analysis are described. The necessity and the expediency of simultaneously application of different linear and non-linear integral transforms during the system spectral analysis performance are explained. The system spectral analysis usage for the ultra-wideband signal time-frequency structure investigation is shown to be effective and useful.