In this talk I present a series of related topics in the mathematical modelling of mass spectrometry data. The presentation opens with a presentation of two algorithms for the generation of the isotopic structure (BRAIN and ISOSPEC).   Then I briefly touch on the problem of understanding Electron Driven reactions, whose principal aim is to induce ion fragmentation. Here I apply the mathematical theory of reaction kinetics to estimate the reaction rates of the electron transfer reactions. Last but not least I present a breakthrough idea to use mathematical theory of optimal transport for molecule identification.