ThermoFisher Center of Excellence in Metabolomics and Exposome Research
Metabolomics has matured over the past 25 years. At UC Davis, we routinely analyze and report on 1,000-2,000 identified metabolites in various biological samples such as plasma, tissue, urine, or cells. This is achieved through meticulous matching of accurate mass, MS/MS similarity, and retention time. Leveraging cutting-edge ThermoFisher equipment, including Orbitraps and triple quadrupole mass spectrometers, we conducted over 80,000 analyses last year alone. Our comprehensive reports encompass details on 34-76 internal standards, levels of confidence in compound annotation, and rigorous quality controls such as method blanks and pooled sample extracts. These reports, which include both raw files and quantification data, exceed the standards set by the metabolomic corporate industry.
In collaboration with ThermoFisher, UC Davis is pushing the boundaries of scientific advancement by integrating targeted methods for absolute quantification into metabolomic and exposome discovery studies.
Utilizing state-of-the-art Astral, IQX, and QE-HF Orbitrap systems, ThermoFisher Scientific and the Fiehn laboratory at UC Davis have showcased the utility of SQUAD methods for simultaneous quantification and discovery in precision medicine approaches and cohort studies, including exposome analyses. The unique capabilities of hybrid instruments enable us to parallelize the acquisition of highly sensitive MS/MS detection of low-abundance compounds, such as lipid mediators and exposome targets, alongside the discovery of novel compound classes. These novel compounds are often absent from typical metabolomic facility reports or industry datasets.
Our integrated LC-BinBase database environment captures all novel compounds in each sample, facilitating their identification through various public and licensed libraries, including GNPS/MassIVE, MassBank of North America, and NIST23. With access to over 4,500 reference standards, we can swiftly confirm new discoveries and validate quantitative reports by incorporating these molecules into UC Davis' targeted methods. Importantly, even unidentified compounds are monitored using unique Spectral Hash Keys and explored across more than 1 billion data reports available through resources such as the West Coast Metabolomics Center servers, GNPS/MassIVE, the European MetaboLights data repository, and the NIH MetabolomicsWorkbench.
These unique identifiers empower clinical and pre-clinical researchers to sift through thousands of studies for comparative analyses and enable cohort research to track and integrate both identified and novel compounds across multiple studies. This integration and quantitative comparison of studies are pivotal in overcoming current challenges in metabolomics and exposome research, ultimately providing insights into the distinctive aspects of chemical exposures and their implications for human health.