Surface-Assisted Laser Desorption/Ionization Mass Spectrometry (SALDI-MS) is a prominent tool for detecting small molecules
however, enhancing its detection sensitivity remains a significant challenge. Two strategies are commonly employed to enhance detection sensitivity: enriching analytes through substrate modification and improving the laser desorption/ionization efficiency of the substrate. In this study, we developed a patterned composite hierarchical structure as a SALDI-MS substrate to improve detection sensitivity. The substrate consists of Si nanopillars and Au nanoparticles, and is patterned with hydrophilic spots and hydrophobic surrounding area. The signal intensity of tetrabutylammonium iodide and sulfacetamide is enhanced by 100-fold and 60-fold, respectively, compared to testing on the Si nanopillars array. The sensitivity enhancement on this substrate is primarily attributed to two factors: first, the analytes are enriched on the hydrophilic spots
and second, the laser desorption/ionization efficiency is improved by the introduction of Schottky barriers through the deposition of Au nanoparticles on Si nanopillars, which extends the lifetime of electron-holes. This design offers high sensitivity, with the lowest detection concentrations for dyes, amino acids and sulfonamides reaching the attomole level. Patterned modifications overcome common issues with super-hydrophobic substrate, such as difficult analyte addition and droplet slippage. The pattern also ensures excellent detection reproducibility, with relative standard deviations (RSD) of 2.4 % across different areas of the same substrate and 6.36 % across different substrates. The substrate is suitable for detecting trace levels of dyes and sulfonamides in river water and seafood extract, demonstrating its potential for analyzing real samples.