Intact molecular ions of the organothiolate-protected nanoparticle Au-25(SCH2CH2Ph)(18), including their isotopic resolution, can be observed at 7391 Da as 1 - and 1 + ions in negative and positive mode, respectively, by MALDI-TOF mass spectrometry when using a tactic of threshold laser pulse intensities and trans-2-[3-(4-tert-butylphenyl)-2-methyl-2-propenylidene]malononitrile (DCTB) as matrix. Previous MALDI-TOF studies of Au nanoparticles using other matrices have encountered extensive fragmentation of nanoparticle as well as thiolate ligands. Absence of fragmentation enables precise determination of the distribution of mixed monolayer compositions on nanoparticles prepared by ligand exchange reactions and by synthesis using thiol mixtures. Reaction conditions producing mixed monolayers containing only one or a small number of usefully functional ligands can be readily identified. At increased laser pulse intensity, the first fragmentation step(s) for the Au-25(SCH2CH2Ph)(18) nanoparticle results in losses of AuL units and, in particular, loss of Au-4(SCH2CH2Ph)(4).