Metabolomics Core

Director: Daniel Kelly, MD

The Metabolomics Core provides critically needed state-of-the-art targeted and untargeted metabolomics and lipidomics services to ACC researchers, which are extremely cost-effective compared to the out-sourcing used in the past.

The Metabolomics Core provides the following:

  • well-validated, quantitative, targeted liquid chromatography-mass spectrometry (LC/MS) metabolomics of 127 metabolites from samples including cells, plasma, and tissues
  • untargeted metabolomics and lipidomics platforms, for metabolite and lipid discovery
  • LC/MS method development for custom metabolite assays tailored to individual needs
  • education and training in the use of the these technologies


Major Services

Cancer cells utilize metabolic pathways distinct from those that predominate in normal cells. Metabolic changes are found across a wide variety of tumor types and are driven in part by specific oncogenic mutations that render cells addicted to their unique metabolism. This "metabolic rewiring" provides an opportunity for intensive and specific metabolomic interrogation of cancer cells. Furthermore, several key-characteristics of carcinogens involve metabolic changes that can be detected in biospecimens, including carcinogen metabolites, DNA adducts, and biomarkers of oxidative stress and inflammation. The Cancer Metabolism Developing Shared Resource was established in 2015 by the ACC to provide essential assays for greater insight into cancer biology and metabolism. Due to the success of the Developing Shared Resource in the current funding period, the Metabolomics Core was established as a full Shared Resource with an expanded array of services to serve the increased needs of ACC members with research efforts ranging from basic to population science. The establishment of this Shared Resource is also cost-effective, as many ACC members had been out-sourcing, which is costly, neglects opportunities for intellectual synergy and collaboration fostered by a Shared Resource on campus and does not allow for the development of personalized assays needed to meet ACC members' research needs. The ACC provided initial support for this Shared Resource along with the Penn Cardiovascular Institute (CVI) and the Institute for Diabetes, Obesity, and Metabolism (IDOM). The scientific rationale for this partnership is founded on established influences of obesity (significantly higher in our catchment area than nationally) and metabolic disorders increasing the incidence of multiple human cancers, importance of understanding environmental carcinogens that promote cancer along with many other diseases, and fruitful collaborations between CVI and ACC in cardio-oncology generally, and its metabolic underpinnings specifically.

The specific services provided by the Metabolomics Core include:

  • Targeted Metabolomics: An LC/MS platform is used to quantify 127 metabolites in cells, plasma, or tissues on an Agilent HPLC/triple quadrupole mass spectrometer. This platform is divided into five separate LC/MS assay modules to maximize extraction recovery and stability from biological samples, chromatographic resolution, and mass spectrometry sensitivity of each metabolite class due to their diverse physicochemical properties. Five distinct assay modules are available together or individually for the measurement of: acylcarnitines (products of fatty acid β-oxidation); amino acids; TCA cycle organic acids; malonyl- and acetyl-coenzyme A (Co-A); and nucleotides. This service is currently being expanded to include assay modules for fatty acids and acyl-CoAs, biogenic amines, organic acids, purines/pyrimidines, glycolysis/pentose phosphate pathway intermediates, bile acids, and redox intermediates for a combined total of over 250 metabolites.
  • Untargeted Metabolomics: A Thermo HPLC/Orbitrap mass spectrometer is used for untargeted metabolomics. This instrument can detect several thousand metabolite signatures (molecular weight 60-1000) in a biological extract, analyze the data to determine statistical differences between study groups, and identify metabolites through a database search.
  • Lipidomics: Untargeted lipidomics is available on an HPLC/Orbitrap mass spectrometer. This instrument can identify several thousand lipid signatures in a biological extract and identify significant lipids through statistical analyses and a database search.
  • Custom Metabolite Assay Development: The Shared Resource develops custom LC/MS assays for specific metabolites to meet individual needs and to validate statistically significant metabolites from untargeted metabolomics experiments by determining absolute metabolite concentrations.
  • Consultation, Training and Education: Dr. Chris Petucci, Technical Director, gives both departmental seminars and lectures in graduate level classes on metabolomics and assay modules to cancer research investigators throughout the year. He and Dr. Dan Kelly, Director, regularly consult with users on experimental design, sample preparation, data analysis and interpretation, and grant and manuscript preparation.

Technologies and Equipment

Instrumentation within the Metabolomics Core includes four triple quadrupole mass spectrometers (Thermo Vantage, two Thermo Ultra AMs, and Agilent 6450) and two high resolution instruments (Q-Exactive HF coupled with regular flow UHPLC dedicated to metabolomics and lipidomics and one coupled to a 2D nano-UHPLC for protein quantification). The Metabolomics Core also has an Agilent 1290 Infinity HPLC and 6495B triple quadrupole mass spectrometer for trace quantitation of metabolites down to the high fg/mL level for targeted metabolomics. In addition, a Thermo Fisher Scientific UHPLC/Orbitrap ID-X mass spectrometer is used for untargeted metabolomics and lipidomics. The high mass resolution (up to 500,000) and low mass accuracy (< 1 ppm) of the Orbitrap provide for enhanced biomarker discovery and structure elucidation of metabolites. Of note, the Metabolomics Core is closely aligned with Penn's Quantitative Proteomics Resource Core, allowing integrated comprehensive metabolomic and proteomic assessments of cells, fluids, and tissues; a unique resource given the importance of regulatory post-translational modifications of histones and other proteins by acetylation, methylation, lactylation, and other metabolites.