Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Master of Science




Konermann, Lars


Electrospray ionization mass spectrometry (ESI-MS) is a powerful technique to investigate proteins and many other analytes. However, many fundamental aspects of ESI remain poorly understood. In this thesis, we use a combination of molecular dynamics (MD) simulations and experiments to gain insights into the hidden complexities of ESI-MS. The structure and reactivity of electrosprayed protein ions is governed by their net charge. In Chapter 2, we sought to uncover the mechanistic basis of La3+-induced charge enhancement. MD simulations showed that irreversible binding via multidentate contacts suppressed La3+ ejection from the vanishing droplets, such that the resulting gaseous proteins carried significantly more charge. In Chapter 3, we examined the supercharging effects of sulfolane on the ESI behavior of salt clusters using similar methods. Spiking NaI solutions with sulfolane resulted in the formation of highly charged cluster ions. MD simulations illustrate that sulfolane stabilizes the cluster to support additional charge. These results demonstrate that the combination of MS experiments and MD simulations can uncover intricate aspects of ESI mechanisms.

Summary for Lay Audience

Proteins are important biological macromolecules that play a key role in virtually all cellular functions. A widely used technique to study proteins is electrospray ionization mass spectrometry (ESI-MS). A protein solution is introduced into the mass spectrometer through a charged capillary, which produces a plume of droplets that subsequently shrink as the solvent evaporates. The droplets contain charge carriers (including H+, Na+ and NH4+) that are transferred to the protein through various mechanisms. The mass spectrometer then detects these charged gas phase proteins. Increasing the charge of these protein ions with solution additives known as “supercharging” agents (SCAs) improves the mass resolution for many experiments. However, the mechanism by which SCAs increase charge is still unclear.

In this thesis, we investigate the role of SCAs using ESI-MS experiments and molecular dynamics (MD) simulations. MD simulations are a computational tool used to model changes in molecular systems. Recently, it has become possible to apply this approach to ESI droplets. Here, we explore how LaCl3 supercharges proteins. Our results show that La3+ tightly binds to the protein early in the ESI process, creating more highly charged protein ions than a singly charged metal counterpart (such as Na+). In a subsequent chapter, we investigate the role of an organic SCA, sulfolane, during experiments on NaI salt clusters. The addition of sulfolane to NaI solution does indeed increase the charge of salt clusters. MD simulations reveal that sulfolane has stabilizing effects that enable the NaI clusters to support additional charge. Our results reveal how MD simulations can explain ESI mechanisms that we cannot investigate using mass spectrometry experiments.