The structure of biomolecules is of fundamental importance to their function and activity. Proteins and peptides adopt three-dimensional conformations that affect every facet of their role in biology ranging from stability, solubility, catalytic and enzymatic interactions, function and dysfunction. These structures are not easily predicted through their primary sequence of amino acids, and there is a strong desire to develop methods for identifying the conformation of biomolecules so that we can better understand biology, disease, and the spectrum of topics and applications that stem from these things. The work embodied in this document represents efforts to build tools that allow us to decipher these structures.

Disulfides can be utilized as receptors for energy transfer from nearby chromophores. The chromophores capable of acting as energy transfer donors include the tyrosine and tryptophan sidechains. Together, this system presents an elegant method to exploit already-present protein chemical moieties in proteins to perform distance-sensitive energy transfer experiments which form the foundation of this work. The excited state of a disulfide bond is a dissociative state, meaning that an intermolecular disulfide receiving energy transfer will result in a mass loss that is detectable by mass spectrometry. This phenomenon is explored in detail, and utilized to extract distance constraints within biomolecular structures. This system, referred to as action-excitation energy transfer (action-EET), is applied to the study of peptides structure, protein structure, and the effects of various conditions such as electrospray solvent on structure. Details about the local solvation environment of the donor chromophore, and special cases such as two-step energy transfer can also be inferred from the action-EET spectra, yielding even more highly specific information that be utilized in structural characterization. This information is then used to guide computations of biomolecule structure to relevant structures to obtain plausible, experimentally-corroborated simulations that are stronger than a purely computational approach. Together, this work presents a useful method for exploring the structure of gaseous biomolecules, as well as a foundation to develop future work in gaseous ion spectroscopy related to energy transfer.