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Expanding the Applications of Ion Mobility Spectrometry and Mass Spectrometry in Integrative ‘Omics Analyses Gregory C. Donohoe Over the past few decades, biomolecular analyses ranging from the study of complex mixtures to protein structural interrogation have increased significantly. These studies range from small molecule separations[1, 2] to observing structural trends in large proteins and protein sub-complexes.[3, 4] Traditionally, the use of liquid chromatography mass spectrometry (LC-MS), electrophoresis and nuclear magnetic resonance (NMR) spectroscopy have been at the forefront of these respective studies. Because complex mixtures can contain a variety of components over a wide dynamic range and proteins and their complexes can contain a diverse array of structures, few analytical techniques are capable of providing information across all experimental areas (e.g. small molecule mixtures to large individual proteins). In contrast, the use of Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) has emerged as a powerful tool for measuring ion(s) structural heterogeneity. While IMS-MS is a relatively newer method, workflows are becoming more common as the commercialization of IMS instruments has created a larger user base. Such workflows now include metabolomic,[1, 5, 6] lipidomic,[7] proteomics and protein structural analyses[8, 9]. Taken collectively, these areas encompass the field of ‘omics’ analysis. While each field has its respective difficulties, IMS-MS is well poised to enhance and even expand the repertoire of analytical platforms for omics analyses. Much of the current bottlenecks in traditional techniques suffer from an inability to sample measureable species rapidly in a reproducible manner over a wide dynamic range. For example, Anderson and coworkers have proposed that the plasma proteome includes 10-10 species that span a concentration range of 10.[10] In many cases, IMS has shown improved resolution of isomeric species compared to either LC or Gas Chromatography (GC) analyses.[11, 12] The utility of IMS-MS in profiling is largely attributed to its rapid ability to resolve low-abundance species from spectral regions containing high-abundance species, thereby increasing measurement sensitivity, dynamic range and peak capacity.[13-17] Additionally, IMS is capable of separating isobaric species that cannot be resolved by MS alone. In 'omic profiling directed toward biomarker discovery, it is imperative to identify compounds of interest. The identification is complicated by compound diversity (class and structural variation). Traditionally, as well as all commercially available, IMS-MS instruments use Time-of-Flight (ToF) mass analyzers for determining an ion’s mass-to-charge ratio (m/z). The obvious advantage is the ability to nest the m/z measurement (μs) within the drift measurement (ms). This creates an orthogonal separation where many m/z measurements are made during the drift separation. Although this combination creates a rapid, multidimensional analysis, ToF mass analyzers are not capable of multistage tandem mass spectrometry (MS) or nonergodic dissociation methods such as electron transfer dissociation (ETD). These MS fragmentation methods are often used as standalone techniques in applications ranging from small molecule identification within complex mixtures to identifying high order structure in proteins using Hydrogen Deuterium exchange (HDX) MS. To this end, new applications of IMS-MS that leverage the use of ion trapping MS are useful for supplementing these limitations of ToF analyzers. Trapping mass analyzers add the capability to perform ion-neutral or ion-ion reactions on drift-selected ions. In such experiments, fragment ions are generated and are structurally useful in identifying and quantifying individual components or those that compose protein structures or post translational modifications (PTMs). To date, very few, if any, experiments have attempted to combine the unique capabilities of IMS-MS with MS or ETD-MS for uncovering ion structural information or heterogeneity. As will be shown in the coming chapters, coupling IMS to trapping mass analyzers expands the capabilities into new areas of ‘omics analysis and enhances the information that can be obtained from either technique alone.

Expanding the Applications of Ion Mobility Spectrometry and Mass Spectrometry in Integrative 'Omics Analyses