In this study, the impact of analyte ablation and substrate surface acidity on ion yield in surface-assisted laser desorption/ionization-mass spectrometry (SALDI-MS) from Pd nanoparticles was examined. The extent of analyte removal from the Pd material was investigated by X-ray analysis and compared to conventional desorption/ionization on silicon (DIOS) and matrix-assisted laser desorption/ionization (MALDI). Despite the different surface morphologies of the investigated materials and the widely varying ionization yields observed during the experiments, virtually the same amount of analyte was removed by laser irradiation from each of the investigated substrates at a given laser fluence. Our experiments therefore suggested that the extent of analyte ablation from the substrate was less important for SALDI efficiency than the chemical properties of the surface.