Laser desorption/ionization mass spectrometry (LDI-MS) has been used to detect gold nanoparticles (AuNPs) in biological samples, such as cells and tissues, by ionizing their attached monolayer ligands. Many NP-attached ligands, however, are difficult to ionize by LDI, making it impossible to track these NPs in biological samples. In this work, we demonstrate that concentrations of matrix-assisted LDI (MALDI) matrices an order of magnitude below the values typically used in MALDI can facilitate the selective detection of AuNPs with these ligands, even in samples as complex as cell lysate. This enhanced sensitivity arises from a synergistic relationship between the gold core and the matrix that helps to selectively ionize ligands attached to the AuNPs.