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We present in this paper a microsystem coupling electrowetting on digital microfluidic and nanostructured surfaces for matrix-free Laser Desorption/Ionization Mass Spectrometry (LDI-MS) analysis of small biomolecules. Silicon nanowires are processed to form highly sensitive pads for LDI analysis and also to produce superhydrophobic surfaces for enhanced transfer of droplets containing the analytes to the analyzing pads. By this way, analysis of low molecular weight compounds with high sensitivity can be achieved. In addition, wetting properties of carbon nanotubes surfaces are investigated in the perspective of further increasing the detection performances.