Time-resolved spectroscopic observations of non-radial oscillations in magnetic Ap stars reveal unexpected and complex pulsation behaviour in spectral lines of individual chemical elements. This diverse rapid spectroscopic variability is closely related to the presence of strong photospheric vertical abundance gradients built up by chemical diffusion. Consideration of chemical stratification and simultaneous interpretation of the pulsational variability of different chemical species have made it possible a tomographic mapping of the radial dependence of pulsation properties of the atmospheres of roAp stars. Combination of the information obtained using pulsation tomography with horizontal mapping using Doppler imaging opens a unique possibility to construct unprecedented three-dimensional maps of pulsation waves, chemical spots and magnetic field in the atmospheres of peculiar A stars.