The ion pair thermal model does not exclude other pathways of ion formation proposed in the literature, and overall charged plume may exist and free ions may contribute to the pool of ions that are detected by the spectrometer. For example, when a sample on a metal substrate is sufficiently thin for laser to reach the substrate or part of the substrate is exposed to the laser radiation, electrons, which have a longer free path than other charged species, in the substrate may escape resulting in excess positive charges at the surface of the substrate and in the sample. Coulombic repulsion leads to desorption resulting an overall positively charged plume. However, in cases that both cations and anions can be detected with similar yields, the pathway involving overall charged plume may play little roles. The following discussions provide estimations of the types and quantities of ions for several classes of molecules commonly analyzed with MALDI MS. The analyses are conducted for both the solid sample and the gas phase. For the latter, the analysis is based on the assumptions of the ion pair thermal model such as thermal equilibrium. MALDI MS ion yields derived from the analysis are close to but probably somewhat lower than experimentally determined values. Before laser irradiation, due to ion stabilization by residue solvents, polar neutral matrix molecules and polar neutral analyte molecules, in solid phase a fraction of the matrices exists in the forms of [M-H] -and [M+H] + . According to the preformed ion emission model, these ions will enter the gas phase upon laser irradiation. Once in the gas phase, the shielding molecules will fall off due to the high temperature, which was estimated to be as high as 2,200 K at the early stage of the plume, 2 and the weakness of the attracting forces between the neutral shielding molecules and the ions. Therefore, there is a strong tendency for the ions [M-H] -and [M+H] + to form the ion pair [M-H] -⁞[M+H] + and go back to M via proton transfer. Both these processes neutralize the ions.