A matrix-free, high sensitivity, nanostructured silicon surface assisted laser desorption/ionization mass spectrometry (LDI-MS) method fabricated by metal-assisted etching was investigated. Effects of key process parameters, such as etching time, substrate resistance and etchant composition, on the nanostructured silicon formation and its LDI-MS efficiency were studied. The results show that the nanostructured silicon pore depth and size increase with etching time, while MS ion intensity increases with etching time to 300s then decreases until 600s for both low resistance (0.001-0.02 Omega cm) and high resistance (1-100 Omega cm) silicon substrates. The nanostructured silicon surface morphologies were found to directly affect the LDI-MS signal ion intensity. By characterizing the nanostructured silicon surface roughness using atomic force microscopy (AFM) and sample absorption efficiency using fluorescence microscopy, it was further demonstrated that the nanostructured silicon surface roughness was highly correlated to the LDI-MS performance. (C) 2010 Elsevier B.V. All rights reserved.