The ion pair thermal model can help to explain several important observations in MALDI MS. The detection of predominantly single-charged ions, which is interesting and a significant advantage of MALDI MS over ESI MS, is one of them. Even for molecules that have multiple easily ionizable groups such as nucleic acids and peptides, single-charged ions almost always predominate. Double-and triple-charged ions may be detected but their peaks are almost always less intense. In the context of the ion pair thermal model, in the plume, there is a strong tendency for the molecules to exist in a neutral form, either through proton transfer or through ion pair. Taking equation (5) for an example, at 1,000 K, for a guanidine group to be protonated and detected, the chance is 10 -4 for Pep-NH + ⁞HSO3 -over Pep-N. At 2,200 K, the number is 3.2 × 10 -2 . For a molecule that contains two such ion pairs, the chance for the molecule to appear as a double-charged peak in MALDI MS is 2.1 × 10 -19 (10 -4 × 10 -4 × 4.6 × 10 -5 × 4.6 × 10 -5 ) at 1,000 K, and 1.2 × 10 -9 (3.2 × 10 -2 × 3.2 × 10 -2 × 1.1 × 10 -2 × 1.1 × 10 -2 ) at 2,200 K. In reality, the chance for detecting doubled charged ions is significantly higher, which indicates that thermal equilibrium may not be fully reached in the plume, and some pre-existed ions in the sample, which have larger inter-ion distance in ion pair after they ejected into the plume, may contribute to the MS signal.