Experimental characterization of the Toffoli gate via channel spectrum benchmarking

Channel spectrum benchmarking (CSB) provides a robust framework for characterizing quantum gate fidelities while remaining insensitive to state preparation and measurement (SPAM) errors. Yet, current CSB implementations encounter fundamental challenges when reconstructing noisy eigenvalues, particularly in the presence of spectral degeneracies and off-diagonal noise components in the target gate's eigenbasis. These issues become especially pronounced in the strong noise regime for gates with fidelities around 90\%. To address these limitations, we introduce an extended CSB model together with a fidelity estimate interval (FEI) - an interval-valued estimate of the target gate fidelity. Numerical simulation demonstrates that FEI remains sufficiently narrow, with its midpoint reliably approximating the true fidelity. We further validate the protocol on a trapped-ion quantum processor by benchmarking two implementations of the three-qubit Toffoli gate. The results reveal a clear advantage of the qutrit-based implementation over its qubit-based counterpart.