Metabolomics Advanced and Applied: Shrinking the metabolomic knowledge gap by advancing and applying metabolomics in integrated multi-omics

Some of the most exciting questions in chemistry lay within the realm of molecular biology. Although different disciplines, throughout history we see chemists and chemical techniques leading the way in important biological discoveries. Metabolomics is a new, developing technique in molecular biology that is spurred on by technical innovations, primarily from the chemistry and engineering fields. Here, two different liquid chromatography mass spectrometry techniques and state-of-the-art bioinformatic tools are employed to help expand the field of metabolomics. In the application phase of this project, metabolomic techniques were applied in a multiomic experiment to elucidate the metabolic pathways used in Staphylococcus. Multi-omics are the coupling of multiple omics techniques such as metabolomics, genomics, and proteomics. In particular, an Ultra-Performance Liquid Chromatography-High Resolution Mass Spectrometry platform was used with a semi-targeted metabolomics technique. Large fold-changes are observed in metabolites mevalonate and phosphomevalonate, which are important distinguishing metabolites between the two isoprenoid synthesis routes. This is used to characterize isolates based on which metabolic pathway they use. This is further verified and expanded by the use of comparative genomics. In the developmental phase of this project, metabolomics techniques were advanced by testing and comparing different extraction methods for multiomic analyses. In this case, chloroform-based extractions were tested against methyl-tert-butyl ether-based extractions to collect metabolites, lipids, and proteins simultaneously. This was analyzed using a High-Performance Liquid Chromatography-High Resolution Mass Spectrometry platform with split-flow nano chromatography and electrospray ionization. Additionally, the cell lysis method is investigated to determine its impact on extraction efficiency and metabolite degradation. Optimizing extraction procedures will make multi-omics faster, easier, and more reliable, thereby facilitating greater use of metabolomics in multi-omics experiments.