Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)



First Advisor

Patrick A. Limbach


The use of mass spectrometry for thermochemical and structural determinations of mononucleotides is presented in Part A of this work, and the analysis of hydrophobic peptides and proteins are presented in Part B of this work. The goal of Part A is to examine thermochemical and structural properties of (deoxy)nucleoside 5'- and 3'-monophosphates. Part A consists of three groups of experiments. The first set of experiments utilized the kinetic method with a fast-atom bombardment source and a double focusing sector mass analyzer. Conformational analysis and semi-empirical calculations of mononucleotides were performed for the second set of experiments. The third set of experiments employed hydrogen/deuterium exchange reactions with an electrospray ionization source and a Fourier transform ion cyclotron resonance mass spectrometer. These data are significant because knowledge of the gas-phase thermochemical properties and structures of nucleobases, nucleosides and nucleotides is crucial in understanding gas-phase reactions of oligonucleotides and DNA observed in current mass spectrometric techniques. The goal of Part B was to develop techniques for the mass spectral analysis of hydrophobic peptides and proteins using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Hydrophobic peptides are difficult to characterize using mass spectrometric methods because they are often insoluble in aqueous solutions, which are typically required for mass spectral analysis. Two approaches were demonstrated. The first approach used organic solvents to dissolve the analyte and matrix to generate signal from a model hydrophobic peptide. The second approach allows for the simultaneous analysis of both hydrophobic and hydrophilic components of the sample mixture by using surfactants to solubilize the hydrophobic components aqueous solutions. Mixtures of hydrophobic and hydrophilic peptides were characterized using surfactant-aided (SA) MALDI-MS, and it is demonstrated that all components are detectable once the surfactant is included in the sample solution. The applicability of SA-MALDI-MS in peptide mapping experiments is demonstrated on a tryptic digest of myoglobin and cytochrome c (two proteins), and on a tryptic digest of CP 43 and CP 47, two hydrophobic polypeptides from the Photosytem II membrane complex of spinach.