An apparatus to generate ions from sample material deposited on a substrate which is at least partially transparent to electromagnetic waves, comprises: —a support device having a holder for the substrate, —a desorption/ionization unit including a desorption device and an ionization device, said desorption device being configured to desorb deposited sample material from a desorption site on the substrate using at least one energy burst, and said ionization device being configured to irradiate the desorbed sample material above the substrate with electromagnetic waves after the at least one energy burst, wherein the electromagnetic waves pass through the substrate before encountering the desorbed sample material at a location which corresponds to the desorption site, and —an extraction device which is arranged and designed to extract ions from the desorbed sample material and transfer them into an analyzer. The invention also relates to a correspondingly arranged method.