2 Principles of Ionization and Ion Dissociation

The mass spectrometer can be regarded as a kind of chemical laboratory, especially designed to study ions in the gas phase [1,2]. In addition to the task it is commonly used for – creation of mass spectra for a generally analytical purpose – it allows for the examination of fragmentation pathways of selected ions, for the study of ion–neutral reactions and more. Understanding these fundamentals is prerequisite for the proper application of mass spectrometry with all technical facets available, and for the successful interpretation of mass spectra because “analytical chemistry is the application of physical chemistry to the real world” [3]. In the first place, this chapter deals with the fundamentals of gas phase ion chemistry, i.e., with ionization, excitation, ion thermochemistry, ion lifetimes, and reaction rates of ion dissociation. The final sections are devoted to more practical aspects of gas phase ion chemistry such as the determination of ionization and appearance energies or of gas phase basicities and proton affinities. Brief discussions of some topics of this chapter may also be found in physical chemistry textbooks; however, much better introductions are given in the specialized literature [4-11]. Detailed compound-specific fragmentation mechanisms, ion–molecule complexes, and more are dealt with later (Chap. 6).