The Ion Pair Thermal Model of MALDI MS

The ion pair thermal model for MALDI MS is described. Key elements of the model include thermal desorption and ionization, strong tendency to neutralization via ion pair formation and proton transfer in the gas phase, thermal equilibrium, overall charge neutral plume, and thermal energy assisted free ion generation via ion pair separation by ion extraction potential. The quantities of ions in the solid sample and in the gaseous plume are estimated. Ion yields of different classes of molecules including peptides, nucleic acids, permanent salts and neutral molecules are estimated at the macroscale and single ion pair levels. The estimated ion yields are close to experimentally observed values under certain assumptions. Explanations of several observations in MALDI MS such as mostly single-charged peaks, improvement of spectra by ammonium cation, and ion suppression are provided. We expect that the model can give insights for the design of new conditions and systems for improving the sensitivity and resolution of MALDI MS and improving its capability and reliability to analyze large biomolecules.