Date of Award

Fall 2013

Degree Type


Degree Name

Doctor of Philosophy (PhD)



First Advisor

Scott A. McLuckey

Second Advisor

Timothy S. Zwier

Committee Chair

Scott A. McLuckey

Committee Member 1

Timothy S. Zwier

Committee Member 2

Lyudmila Slipchenko

Committee Member 3

R. G. Cooks


A new instrument incorporating ion trap based tandem mass spectrometry and cold ion UV and UV-IR double resonance spectroscopy has been developed at Purdue University for the study of gas phase, biologically relevant ions. The instrument incorporates multiple quadrupole linear ion trap mass analyzers to prepare and isolate the precursor ions as well as to analyze the resultant photofragments. A 22-pole ion trap cooled to 5 K via a closed cycle helium cryostat is used to cool the ions for spectroscopic interrogation. Results show the vibrational and rotational temperature of a wide assortment of ions to be 12±2 K.

The capabilities of the instrument are confirmed using the protonated amino acid tyrosine (Tyr), following precedent established in the literature. The UV spectrum shows 12±2 K ion temperatures and signal to noise comparable to previous studies presented in the literature. A novel mode of UV photofragment spectroscopy is presented which allows for the observation of all photofragments, whereas previous methods observe the fragmentation of a single mass channel.

The infrared capabilities of the instrument are proven using the model pentapeptide leucine enkephalin (sequence YGGFL). Infrared spectra demonstrate a single conformation being present, with a reinforced hydrogen bonding scheme involving the N- and C-terminal groups. A novel mechanism for obtaining IR spectra of all conformations present in an ion population is demonstrated, with significant increases in signal to noise when compared to depletion type measurements.

A novel, miniaturized ion funnel type ion funnel is briefly described. The ion funnel is compatible with established ion sources within the laboratory and demonstrates a ~7x increase in ion signal. Briefly, data and considerations regarding cold ion spectroscopy within a modified 3D ion trap is presented. Ion temperatures were found to be limited to a minimum of 50 K due to the additional RF heating associated with a quadrupolar trapping field.