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Radical chemistry represents a powerful set of reactions in which unstable odd electron species can undergo rapid and spontaneous chemical rearrangements. These reactions have recently found analytical use in the dissociation of peptides and proteins in mass spectrometry. In this dissertation, the factors controlling radical migration and dissociation are explored in detail through examination of model peptides and proteins by mass spectrometry and quantum mechanical calculation. Understanding the behavior of radicals in proteins is key to being able to further enhance their analytical usefulness. Radicals already play an important role in electron capture dissociation (ECD) and electron transfer dissociation (ETD) mass spectrometry. When applied to peptides both gas phase dissociation methods yield nearly complete and uniform sequence coverage while retaining labile post-translational modifications (PTMs). In contrast, a recently developed technique, radical directed dissociation (RDD), induces fragmentation at very specific locations in derivatized peptides and proteins which has proven useful in a variety of applications including the facile identification of PTMs. RDD provides very specific fragmentation and is complimentary to the broad uniform fragmentation provided by ECD/ETD. Despite these differences in observed dissociation patterns, ECD, ETD, and RDD are all driven by radical chemistry. This disparity in observed fragmentation can be explained by radical conversion and migration.Radical migration in peptides typically occurs via hydrogen atom abstraction. In this manner radicals may travel to different sites within a …