Determining the Structures and Properties of Biologically-relevant Ions

Gas phase studies of biologically relevant ions are increasing in popularity due to the possibility of high throughput analysis requiring minimum sample concentrations. This thesis explores the potential of differential mobility spectrometry-mass spectrometry (DMS-MS) in combination with quantum chemical calculation methods to probe the structures, energetics, and dynamics of three distinct classes of biomolecules. The first project outlines the use of DMS-MS to separate and identify protonated forms of methylated and unmethylated nucleobases to gain a fundamental understanding of their gas phase properties in relation to their role in nucleic acids. Next, DMS-MS and calculations were conducted for a large RNA system, the Varkud Satellite ribozyme active site loop VI, to study differences between its active and inactive conformations, especially through the use of negative mode hydrogen-deuterium exchange. Finally, DMS-MS was used to identify transformation products of trimethoprim, an antibiotic often found in environmental wastewaters in a reliable and efficient method. Ultimately, DMS-MS and quantum calculations have been shown to be a powerful analytical tool to investigate structures and properties of biomolecules. The methodologies described herein can have an impact in a wide variety of industries, from drug discovery to environmental wastewater cleanup

Identifying Fenton-Reacted Trimethoprim Transformation Products Using Differential Mobility Spectrometry

This document is the Accepted Manuscript version of a Published Work that appeared in final form in, copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acs.analchem.8b00484.A transformation product of trimethoprim, a contaminant of emerging concern in the environment, is generated using an electro-assisted Fenton reaction and analyzed using differential mobility spectrometry (DMS) in combination with MS/MS techniques and computational calculations to develop a rapid method for identification. DMS is used as a pre-filter to separate positional isomers prior to subsequent identification by mass spectrometric analyses. Collision induced dissociation of each DMS separated species is used to reveal fragmentation patterns that can be correlated to specific isomer structures. Analysis of the experimental data and supporting quantum chemical calculations show that methylene-hydroxylated and methoxy-containing phenyl ring hydroxylated transformation products are observed. The proposed methodology outlines a high-throughput technique to determine transformation products of small molecules accurately, in a short time and requiring minimal sample concentrations (<100 ng/mL).NSERC Discovery Grant 30345

Separating and probing tautomers of protonated nucleobases using differential mobility spectrometry

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.ijms.2017.08.008 © 2017. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/The protonated nucleobases (C+H)+, (T+H)+, (U+H)+, (A+H)+, and (G+H)+ are investigated in a combined experimental and computational study using differential mobility spectrometry (DMS), mass spectrometry, and electronic structure calculations. DMS is used to isolate individual tautomeric forms for each protonated nucleobase prior to characterization with HDX or CID. The population distributions of each protonated nucleobase formed by electrospray ionization (ESI) are dominated by a single tautomeric form, as is predicted by our calculations. However, all nucleobases present additional tautomers upon ESI, with these minor contributions to the ensemble populations attributed to additional higher energy metastable species. In addition to the tautomer-derived species, additional ion signals in the DMS data are attributed to larger nucleobase-containing clusters, which fragment post-DMS to yield bare ion and fragment ion signals that are consistent with those expected for the bare protonated nucleobases. Contributions from larger clustered species are instead distinguished by monitoring DMS ion signal as declustering potential voltages are ramped.Natural Sciences and Engineering Research Council (NSERC) of CanadaDiscovery Grant, Collaborative Research and Development Grant programsOntario Centres of ExcellenceVIP-II gran

Identifying Fenton-Reacted Trimethoprim Transformation Products Using Differential Mobility Spectrometry

A transformation product of trimethoprim, a contaminant of emerging concern in the environment, is generated using an electro-assisted Fenton reaction and analyzed using differential mobility spectrometry (DMS) in combination with MS/MS techniques and quantum chemical calculations to develop a rapid method for identification. DMS is used as a prefilter to separate positional isomers prior to subsequent identification by mass spectrometric analyses. Collision induced dissociation of each DMS separated species is used to reveal fragmentation patterns that can be correlated to specific isomer structures. Analysis of the experimental data and supporting quantum chemical calculations show that methylene-hydroxylated and methoxy-containing phenyl ring hydroxylated transformation products are observed. The proposed methodology outlines a high-throughput technique to determine transformation products of small molecules accurately, in a short time and requiring minimal sample concentrations (<25 ng/mL)