We have evaluated the laser desorption ionization mass spectrometry (LDI-MS) performance of six nanostructured silicon surfaces of different morphologies and chemical functionalizations. The substrates have been synthesized either by metal-assisted etching method or by vapor-liquid-solid (VLS) growth technique. In addition to the commercial nanostructured silicon-based surface (NALDI) target plates, serving as reference, the homemade surfaces have been evaluated in mass spectrometry experiments conducted with peptide solutions mimicking tryptic digests. LDI surfaces synthesized by metal-assisted etching method were the most efficient in terms of signal intensities and number of detected peptides. The surface providing the best LDI-MS performance was composed of two nanostructured layers. Interestingly, we also observed a significant influence of the type of organic coating (hydrocarbon vs fluorocarbon) on peptide ionization discrimination.