Protonation Isomers in Mass Spectrometry: Ionization, Ion Chemistry, and Interconversion

Abstract Protonation isomers (protomers) are structural isomers that differ in the location site of a proton (H+). In mass spectrometry, an understanding of the fundamentals of analyte protonation is essential as the site of protonation influences many gas-phase ion properties, including ion stability, ion fragmentation yields and products, ion–molecule reactivity, photochemistry, conformation, and chirality. If ignored, the presence of protomers can confound the detection and assignment of analyte ions and can also reduce peak loading under many mass spectrometry workflows. In this perspective, we outline how small-molecule protomers arise and discuss the competing mechanisms that govern their relative populations, this implicates electrospray droplet desolvation, ion source reactions, proton-bound dimer stability, ion–molecule reactions, collision-induced internal proton transfer, and photoinduced internal proton transfer. Key concepts are summarized and frontiers for charge-site management are proposed, including deprotonation isomers, metal cations, and multiply charged species.