Date of Award

Fall 2013

Degree Type


Degree Name

Doctor of Philosophy (PhD)



First Advisor

Scott A. McLuckey

Committee Chair

Scott A. McLuckey

Committee Member 1

Hikka I. Kenttamaa

Committee Member 2

Tong Ren

Committee Member 3

Garth J. Simpson


Analytical mass spectrometry has been widely applied in the field of biomolecule identification and characterization. It provides fast, accurate and robust information relevant to the molecular mass, composition and structure of the target analytes.

This thesis is focused on the top-down analysis of various macrobiomolecules, nucleic acids and proteins, in the context of ion/ion reaction and gas-phase unimolecular dissociation. The first part of the thesis deals with gas phase fragmentation behavior of chemically modified oligonucleotides. Factors, such as the observation time-scale, the ion type and the energy deposition method, are explored using a quadrupole/time-of-flight mass spectrometer. Novel fragmentation pathway associated with negative electron transfer dissociation has been investigated and applied to heavily modified siRNA analogues to increase the amount of sequence information that can be derived from the mass spectrum.

The second part of this thesis discusses proximity mapping using chemical crosslinking mass spectrometry coupled with ion/ion reaction. Crosslinkers with various linker arm lengths have been used to probe the proximity between the lysines on the surface of a folded protein. This approach has proved to be a rapid way to generate low-resolution structure information with significantly small sample quantity.

The last part of the thesis is focused on ion manipulation techniques in the mass spectrometer to increase the sensitivity and selectivity of the ion/ion reaction. Ion evaporation mechanism of the dipolar DC mechanism has been studied to understand the effective high mass limitation in the dipolar DC experiment. Efficient ion parking has been implemented in a linear ion trap with the help of axial DC gradient.