Developing Trapped Ion Mobility Spectrometry as a Tool for the Structural Elucidation of Biological Compounds

One of the grand challenges in the field of human health is to understand the structure-function relationship of biological molecules. To date, there exist many types of low and high resolution methods for interrogating the structure of biological monomeric and assembly systems. No one structural technique is up to the challenge in elucidating the detailed three dimensional structure of every analyte of interest. A culmination of structural data collected by an assortment of methods is the only approach in overcoming the diverse limitations that inevitably plague each technique. Ion mobility mass spectrometry (IMS-MS) certainly occupies an area in the spectrum of structural elucidation platforms. IMS-MS has certain advantages other techniques that make it a powerful tool for studying the structure of biological complexes. Trapped ion mobility spectrometry (TIMS) is a recently developed and commercialized high resolution ion mobility technique. TIMS as a new method must be validated in its ability to probe the biologically relevant structures of biological molecules and their assemblies. My work in the Bleiholder lab began with working on a project that showed for the first time that native like conformers of the protein ubiquitin could be retained during the course of a TIMS analysis. The remainder of this document seeks to continue to develop TIMS as a useful tool for structural biology. Chapter one gives a brief and general overview of some of the structural methods available to date, and presents some of the details related to ion mobility and TIMS. Chapter two shift from preserving monomeric to multimeric systems in TIMS. We show there that inadvertent fragmentation leading to structural artefacts can be overcome. Chapter three shows as a proof of concept that tandem-TIMS can perform CID of proteins up to ~18 kDa. We show that TIMS-CID-TIMS can not only provide sequence coverage similar to other mass spectrometry platforms, but that it also can sample conformational differences between fragments of the same m/z ratio. Chapter four exhibits the ability of tandem-TIMS to thermally unfold the protein ubiquitin in the electrospray source. Chapter 5 seeks to characterize the trapping efficiency of the TIMS analyzer and shows ions can be retained for upwards of 15 seconds. Finally chapter six provides a conclusion and future direction. Additional details in the aforementioned chapters are found in the appendices.