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The ATOMS Core enables innovative research at UNC-Chapel Hill by providing equipment, expertise and training in small molecule applications utilizing mass spectrometry in an open-access facility.

We proactively build relationships with UNC departments and researchers (both internal and external) to acquire, support and operate mass spectrometry capabilities that are critical for their current and future research success.

The ATOMS Core laboratory specializes in small molecule metabolomic and lipidomic applications.  We offer a diverse array of experimental approaches that can be tailored to meet your analytical challenges.  From global metabolomics to targeted lipid panels, our methods are robust and well-characterized to meet the rigor and reproducibility standards required in today’s research environment.

The ATOMS Core is located in the UNC Department of Chemistry Mass Spectrometry Laboratory.


The ATOMS Laboratory Staff are perpetually available to discuss experimental design and the sample submission process.  It is our Core’s preference that we conduct sample extractions and sample preparations prior to analysis on our mass spectrometers. Please reach out to us with any and all questions.

  • Polar Metabolite Panel—our expandable polar metabolite panel currently consist of ~230 metabolites routinely utilized by common cellular pathways, such as the Krebs Cycle, the urea cycle, the fatty acid synthesis pathway, as well as the amino acids. Identification of metabolites results in generated p-values with KEGG IDs for pathway analysis.

Examples: cell mechanistic studies, flux-omics, WT vs Mutant investigations

  • Non-polar” Metabolite Panel—this untargeted LC-MS experiment is less bias than the polar metabolites panel and captures a broader array of metabolites in each sample. This method is amenable to small polar compounds and larger non-polar compounds. Potentially captured metabolite classes include: amino acids, alkaloids, fatty acids, and small lipids. The data processing approach here is intense and requires a large portion of personnel time. An untargeted online library database search will be conducted along with univariate and multivariate statistical analysis. This analysis is ideal for experiments where little is known about the sample set or situations where there are specific groupings of samples with detailed conditions.

Examples: different growth conditions, WT vs Mutant investigations with large populations and variations, complex clinical datasets (kidney disease, lung disease, cancer, etc)

  • Global Metabolite Panel—the most powerful combination of metabolite identification we offer combines both the polar (a) and “non-polar” (b) metabolite panel and generates one large dataset. This assay takes longer to generate data and to process but provides an exhaustive view of metabolites in each sample.
  • Untargeted Lipidomics—this assay is designed to acquire data on many individual lipid species and compare abundances between experimental conditions (e.g., drug vs DMSO, knockout vs. wild type, etc.). Comparison between conditions requires a minimum of three biological replicates per condition. Lipids are separated by hydrophobicity using reverse-phase liquid chromatography and introduced to the MS using electrospray ionization (ESI). DDA provides a combination of high resolution, accurate mass data at the MS1 level (which can suggest molecular formulas) and structural information obtained at the MS2 level (which can suggest connectivity within a molecule) that can be used to identify lipid species.
  • Short Chain Fatty Acids—this group of fatty acids are derived from intestinal gut microbiota during the fermentation of partially- and non-digestible foods. Our assay aims to identify and quantify 9 of the most-common short and branched chain fatty acids: acetic, propionic, isobutyric, butyric, isovaleric, 2-methylbutyric,valeric, 3-methylvaleric, 4-methylpentanoic, and hexanoic acid. Utilizing gas chromatography mass spectrometry we are able to identify and quantify the level of each fatty acid in each sample.
  • Fatty Acid Methyl Esterification (FAME)—the fatty acid methyl esterification assay extracts lipids and transesterifies free fatty acids in the extract to improve their volatility making them more amendable to separation and detection utilizing gas chromatography mass spectrometry methods. Presently, we are able to detect and quantify up to (37) fatty acid methyl esters per sample.
  • Targeted Lipid Assay—we customize and collaboratively create targeted quantification assays to interrogate narrow regions of the lipidome. Currently we have functional assays in polyunsaturated fatty acids (PUFAs), phosphatidic acid, and a broad steroid panel.  Please consult with us about your experimental needs and we will work to create a custom assay for your research.
  • Targeted Metabolite Assay— we customize and collaboratively create targeted quantification assays to interrogate narrow regions of the metabolome.  Please consult with us about your experimental needs and we will work to create a custom assay for your research.


Brandie Ehrmann, PhD

Director, ATOMS Core

131 South Road
Caudill 022
Chapel Hill, NC 27599