Mass Spectrometry-based Untargeted Metabolomics

National Institute Of Environmental Health Sciences

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Abstract

The Metabolomics Core Facility (MCF) performed research on a wide variety of projects during this period in support of the objectives of the NIEHS and NIH. The MCF analyzed >2100 unique samples from 12 NIH ICs. Research was performed with 35 unique investigators and more than 70 different researchers. The primary effort this year was performing untargeted metabolomics analysis while concurrently improving upon untargeted metabolomics methods developed in the prior year (including protocols for sample extraction, data acquisition, and data analysis). An untargeted metabolomics method has implemented using a reverse-phase liquid chromatography - mass spectrometry approach. The data are collected using a data-dependent method (DDA) in which MS1 and MS/MS information (used in identification) are collected concurrently. Over 600 chemical standards were analyzed, interpreted, and compiled into an MS/MS spectral database for annotation. This same approach has been adapted to utilize hydrophilic interaction chromatography (HILIC), in substitute for reverse-phase chromatography, for the analysis of polar metabolites. Using the developed untargeted metabolomics methods, the MCF has analyzed samples from cell lines, animals, and humans in support of basic, translational, and clinical research. The types of samples the MCF analyzed include cancer cells, macrophages, platelets, yeast, blood plasma, blood serum, urine, perilymph, saliva, brain, liver, lung, liver, muscle, fecal, tongue, placenta, and others. A typical experiment results in the annotation (putative identification) of approximately 5-10% of all measured chemical signals. Such results are on par with established metabolomics cores and academic laboratories performing LC-MS based metabolomics analyses. Further, the MCF support investigators by processing, analyzing, and interpretating metabolomics data. We have developed in-house R scripts and Jupyter Notebooks to facilitate data analysis, quality assurance, and quality control procedures including pooled quality control measures, signal response evaluation, dispersion ratio, and others. The result is a robust, high-quality untargeted metabolomics data acquisition method and data processing pipeline to serve NIEHS and NIH investigators. To better serve the research needs, we have dedicated substantial time and resources to developing targeted metabolomics assays which will support metabolomics research. This develop was made possible by a new state-of-the-art triple quadrupole mass spectrometry system installed in the prior fiscal year. With this capability, the MCF can quantitatively measure metabolites (and exogenous chemicals) in biological samples. This provides NIEHS and NIH investigators access to unique, customizable measurement solutions to address biological and biomedical hypotheses.