Development of Ion Mobility and Mass Spectrometry Strategies in Support of Integrated Omics and Systems Biology

Abstract

Systems biology greatly enhances the study of complex biological processes by expanding on reductionist approaches that have traditionally focused on individual biological components (i.e. glycomics). Systems biology strategies allow for the comprehensive analysis of biological samples as a whole. To advance these systems analyses strategies, we have developed ion mobility-mass spectrometry (IM-MS) techniques to study biological systems in the gas phase through class specific structural separations. Proteins, lipids, and carbohydrates, which exhibit overlapping signals in a 1-D mass spectrum, are separated in IM-MS because each biomolecular class occupies a unique region of conformational space. Thus, IM-MS analysis is able to differentiate molecules present in complex biological samples with minimal sample purification, greatly improving upon current methodologies. Here, a simple LC-IM-MS method for non-derivatized glycans was described for simultaneous glycomics and proteomics analyses. Glycans released from fetuin were separated on a reverse phase column such that analyses were compatible with proteomics workflows. Novel sequencing workflows were developed utilizing multi-modal fragmentation techniques to obtain finer structural detail of glycoconjugates and glycoproteins. These multi-modal techniques were applied to a carcinoembryonic antigen and show great promise as a more comprehensive sequencing strategy. As many metabolites of interest are decorated with carbohydrate and peptide moieties, parallel studies aim to develop technologies to address the challenges associated with the analysis of these structurally unique small molecules. High throughput chip-based HPLC-IM-MS technologies are well suited for metabolite analysis and lead target prioritization. A series of small molecules were analyzed by chip-based HPLC-IM-MS to compile a database of four-dimensional descriptors to assist dereplication efforts. IM-MS provides broad scale biological structural descriptors, which can be further honed to describe subclass and multiclass descriptors. Combining broad and fine structural studies in this manner creates a toolbox for extensive analyses of metabolomics, glycomics and more generally, integrated omics at large.