We show how two frequency combs E1, E2 can be used to measure single-photon, two-photon absorption (TPA), and Raman resonances in a molecule with three electronic bands, by detecting the radio frequency modulation of the nonlinear transmission signal. Some peaks are independent of the carrier frequency of the comb and others shift with that frequency and have a width close to the comb width. TPA and Raman resonances independent of the carrier frequency are selected by measuring the transmission signal ∼E12E22 and the single-photon resonances are selected by measuring the transmission signal ∼E13E2. Sinusoidal spectral phase shaping strongly affects the TPA, but not the Raman resonances. © 2014 American Physical Society.