Structural analysis of biomolecules using ion mobility and mass spectrometry : exploration of ion rearrangements and conformations.


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Early diagnosis of diseases is dependent on the development of reliable physiological and biochemical tests. The most precise medical tests employ analytical methods to identify specific molecules (“biomarkers”) or molecular signatures (“biomarker panels”) to monitor physiological responses to disease progression. It is conceivable that, one day, every disease could be classified by monitoring changes in biomolecular compositions. To realize this goal, however, it is necessary to develop highly sensitive tools that are capable of providing structural information about minute components of complex mixtures at the molecular and biologically relevant levels. Currently, mass spectrometry (MS) is the most suitable technique for routine and comprehensive molecular characterization of complex samples such as blood, saliva, urine, and tissue. Although MS is a promising tool for clinical diagnosis of diseases, ion rearrangements and presence of structural isomers can limit its utility. In this dissertation, results from investigations of ion rearrangements and biomolecular structures, using cutting-edge MS and ion mobility (IM)-MS techniques, are presented. In Chapter One, the operating principles of various types of mass and IM spectrometers, and their applications to analysis of biomedical systems, are discussed. Next, results from isotope labeling, tandem mass spectrometry, and IM-MS are presented to demonstrate that losses of internal backbone carbonyls from y-type peptide ions are intermediate steps towards the formation of rearranged fragment ions (Chapter Two). In Chapter Three, MS, IM-MS, and theoretical modeling data are presented to demonstrate that collision-induced dissociation (CID) of 5′ phosphorylated DNA can generate rearranged [phosphopurine]- product ions. Limited IM resolving powers may hinder adequate characterization of conformationally similar ions and reduce the accuracy of IM-based collision cross section (CCS) calculations. In Chapter Four, chemometric deconvolution of post-IM/CID MS data is used to extract IM drift times (DTs) of IM-unresolved isomers. Extracted DTs are used to calculate CCSs that are comparable to CCSs calculated from individual analysis of each isomer using traveling wave and drift tube IM-MS and the superposition approximation (PSA) molecular modeling. Finally, in Chapter Five, future directions and preliminary results from application of techniques discussed in Chapters One through Four to rapid analysis of tissue is presented and discussed.



Mass spectrometry (MS). Ion mobility-mass spectrometry (IM-MS). Rearrangement. Sequence-scrambling. Fragmentation. Collision-induced dissociation (CID). Collision cross section (CCS). Deconvolution. Structural isomers.