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Collision cross sections of gas phase DNA ions Moradian, Annie

Abstract

The aim of this work is to study the collision cross sections of single stranded DNA ions in an electrospray ionization (ESI) mass spectrometer (MS). In part this work was motivated by a fall-off in signal intensities in ESI-MS with increasing molecular weight of the DNA. The first part of this thesis discusses the theories and experimental methods of measuring and calculating collision cross sections of bio-molecules. The collision cross section is a measure of ion "size" which can provide direct insight to structural characterization of bio-molecules. The second part of this thesis describes experiments with 28-, 40- and 55-mer oligodeoxynucleotide ions and protein ions of nearly the same molecular weight— ubiquitin, cytochrome c and apomyoglobin. The energy losses of ions from collisions with argon were measured and interpreted with a diffuse scattering model. The last part of this thesis presents the comparison of cross sections of oligodeoxynucleotides with cross sections of the proteins. The oligodeoxynucleotides produce negative charge states in ESI similar to he positive charge states produced by the proteins denatured in solution. Cross sections for oligodeoxynucleotide ions increase with charge state similar to those of protein ions. For a given molecular weight and charge state, the cross sections of the oligodeoxynucleotide ions are about 22% lower than those of the proteins. In this study, ESI mass spectra of 28-, 40- and 55-mer oligodexoynucleotides show similar sensitivities and a fall-off in signal intensity with increasing mass has not been observed.

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