Gold nanoparticles (AuNP) are frequently used in surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) for analysis of biomolecules because they exhibit suitable thermal and chemical properties as well as strong surface plasmonic effects. Moreover, the structures of AuNP can be controlled by well-established synthesis protocols. This was important in the present work, which studied the influence of the nanoparticles' structures on atmospheric pressure (AP)-SALDI-MS performance. A series of AuNP with different core sizes and capping ligands were investigated, to examine the desorption/ionization efficiency (DIE) under AP-SALDI conditions. The results showed that both the AuNP core size as well as the nature of the surface ligand had a strong influence on DIE. DIE increased with the size of the AuNP and the hydrophobicity of the ligands. Chemical interactions between ligand and analytes also influenced DIE. Moreover, we discovered that removing the organic ligands from the deposited AuNP substrate layer by simple laser irradiation prior to LDI further amplified DIE values. The optimized AuNP were successfully used to analyze a wide arrange of different low molecular weight biomolecules as well as a crude pig brain extract, which readily demonstrated the ability of the technique to detect a wide range of lipid species within highly complex samples. 1 INTRODUCTION Since cobalt nanoparticles were first used for surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) by Tanaka et al, 1 nanomaterials made from carbon, 2-4 silicon, 5-7 metals (Au, Ag, Pa, etc.), 8-10 metal oxides, 11-13 and others materials 14-17 have been successfully applied to SALDI-MS. In general, nanoparticles are excellent substrate options for SALDI, because they require only simple and easy sample preparation techniques and the materials often exhibit minimal background signals-in particular in the low m/z range-as compared to matrix-assisted laser desorption/ionization (MALDI). 18-20 SALDI efficiencies can be enhanced by optimizing the nanoparticular structures, for example, by modifying the core size and nature of the surface ligands, 18 which was shown to be vital for sensitive quantitative analysis of biomolecules. 20 In previous studies, it was found that desorption/ionization efficiency of SALDI was highly dependent on physical (size, surface roughness, light absorption, electrical conductivity, melting point, etc.) and chemical (surface modification, binding energy to analytes, etc.) properties of the nanomaterials. 18-23 Gold nanoparticles (AuNP) exhibit excellent electrical conductivities, thermal and chemical stabilities and strong light This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. c