Metabolomics Core Facility

File Internal UIowa Sample Submission Form

For external price information, please inquire. 

Sample prepation guidelines below.

Mission Statement

The Fraternal Order of Eagles Diabetes Research Center (FOEDRC) Metabolomics Core Facility (Core) utilizes state-of-the-art GC-MS and LC-MS mass spectrometry to perform metabolomic analysis of biological samples. The Core serves University of Iowa researchers as well as external academic and private institutions. Scientists at the Core are committed to providing outstanding service to help investigators solve basic and clinically relevant biological problems.  

What We Do: 

We provide full service metabolomic analysis, from receipt of frozen samples through return of tabulated, numerical data representing metabolite abundances. We work closely with investigators to select metabolomic services depending on their scientific goals. We consult on experimental design and sample preparation to retain the in vivo metabolome, enhance reproducibility, and obtain adequately powered data. All services are Tier 1, utilizing spectral libraries generated in-house by running physical standards. 

When beginning a metabolomic investigating, we often suggest starting with our well-established GC-MS panel, which surveys key metabolites across several major biochemical pathways.   

Our GC-MS panel is the front end of a “smart”, data-informed modular workflow, where depending on results, the remaining sample extract can be analyzed by LC-MS for a detailed investigation of metabolite classes not amenable to GC-MS.  

Alternatively, for investigators seeking maximal metabolomic coverage from the start, we offer broad LC-MS profiling services. This service covers most metabolites in the GC-MS panel and all metabolites in the LC-MS modules except for bile acids and short chain fatty acids. 

To provide mechanistic, pathway-specific information on substate utilization, we perform stable isotope enrichment and mass isotopologue abundance analysis for metabolic tracing experiments.  


Broad Metabolomic Profiling:

Broad GC-MS Metabolite Profiling:  Survey of central carbon metabolism measuring metabolites in glycolysis, the pentose phosphate pathway, the TCA cycle, and neurotransmitters, amino acids, fatty acids, and others (~100 compounds, depending on the type of sample).

Deep LC-MS Metabolite Profiling: Deep coverage of central carbon metabolism and peripheral pathways, 250-300 compounds, depending on the type of sample

Specialized LC-MS Modules:

High Energy Redox: Coverage of 72 metabolites including redox co-factors, nucleotide, and high-energy phosphates, and acyl-CoAs.

Acyl-Carnitines: Carnitine, acetyl-carnitine and 13 other acyl-carnitines from propionyl to arachidonylcarnitine (C20:4).

Short Chain Fatty Acids:  Streamlined acquisition for acetic, propanoic, and butyric acids.

Bile acids: 16 bile acid species including alpha-MCA, CDCA, CA, DCA, GCDCA, GCA, GDCA, GLCA, GUDCA, LCA, TCDCA, TCA, TDCA, TLCA, TUDCA and UDCA.

Isolated Mitochondria TCA Cycle: Pyruvate, acetyl-CoA, TCA cycle intermediates, and adjacent amino acids alanine, aspartate, glutamate, and glutamine. Analysis only for isolated mitochondria. 

Plasma Glucose Trace/Derivatives: Mass isotopologue distribution analysis of glucose or glucose-derivatives in plasma.

LC-MS Isotope Tracing analysis: 

Stable isotope enrichment and mass isotopologue abundance analysis is a powerful method for dissecting pathway-specific substrate trafficking and measuring metabolic processes. Examples of use include measuring gluconeogenesis, de novo lipogenesis, and amino acid catabolism (many others). We trace compounds labeled with 13C, 15N, 2H, or 18O. If you are interested in stable isotope tracing analysis, please consult with us before beginning your experiment.  


  • Thermo ISQ LT GC-MS:

The ISQ LT GC-MS is a single quadrupole mass spectrometer with a Trace 1310 GC and a RSH autosampler. The GC-MS is used for profiling of over 100 (and continuously expanding) in-house standard verified metabolites for Tier 1 identification. Specialized software is used to compare relative metabolite abundances between samples.

  • Thermo TSQ GC-MS:

The TSQ is a triple quadrupole mass spectrometer with a Trace 1310 GC with the same autosampler as the ISQ. This mass spectrometer can perform tandem mass spectrometry (MS/MS). Data is collected by an MS/MS scanning method known as multiple reaction monitoring or MRMs, which are routinely used for trace level detection of targeted metabolites. Similar to the ISQ, this GC-MS is used for broad metabolite profiling for over 100 in-house standard metabolites for Tier 1 identification.

  • Thermo Q Exactive LC-MS:

The Core has two Thermo Q Exactive LC-MS systems (QE-LC) which are hybrid quadrupole-Orbitrap mass spectrometers interfaced with a Vanquish ultra-high pressure liquid chromatography (UHPLC) system. This mass spectrometer is a high-resolution accurate mass (HRAM) Orbitrap mass spectrometer with maximum resolving power of 140,000 or mass accuracy <1 ppm with internal standard. The Vanquish UHPLC system includes a binary solvent pump, column heater, and autosampler. The QE-LC can perform tandem mass spectrometry (MS/MS) experiments, which provides options for qualitative and quantitative applications. The QE-LC is especially useful for measurement of high energy/redox species, coenzymes, lipids, and other metabolites not amendable to GC-MS methods and is used for stable isotope tracing analysis. The Core has generated an in-house MS/MS library, using authentic standards to confirm identification of targeted metabolites by accurate mass, retention, and matching MS/MS spectra.

Quality Insurance and Quality Control

  • Quality Insurance: To insure quality, instruments are maintained through weekly upkeep and regular vendor provided (Thermo) preventative maintenance, with emergency on-site maintenance available within 72h of a request. Mass spectrometers are calibrated at recommended intervals, and every run includes an aliquot of a large stock human plasma sample to quantify run consistency. Submitted samples are processed using clearly delineated standard operating procedures (SOPs). When an SOP is updated, it is given a new identifier, and past SOPs are permanently archived and available to customers upon request.   
  • Quality Control: Critical aspects of this quality control management include use of isotopically labeled standards during sample extraction, and use of an experiment-specific pooled quality control sample that is run repeatedly between every 5th to 10th experimental sample to detect instrument drift and enable correction. The core also utilizes targeted metabolomic spectral libraries generated in-house by running authenticated standards for Tier 1 identification, and multiple levels of computational filtering and exclusion for untargeted metabolomics.  

Sample Preparation Guidelines

For tissue:

Weigh out 40mg of tissue in liquid nitrogen making sure the samples remain frozen until delivery. Please ensure that all samples are within 10mg of each other. Samples should be delivered in 1.5ml micro-centrifuge tubes.

For plasma and serum:

Provide 40µl plasma/serum frozen in 1.5 ml micro-centrifuge tubes and deliver on dry ice. Please ensure that all volumes are consistent.

For plated cells:

Whole cells should be washed twice on plates with ice-cold PBS, then twice with ice-cold water. Freeze cells by floating the plate on liquid nitrogen: hold the plate above the liquid phase for a few seconds to prevent the plate from cracking. Well-powered experiments generally require at least 6 replicates per condition. For many cell lines, nearly-confluent 6-well plates provide enough sample to obtain full metabolite coverage.


Contact Information

1. Eric Taylor, PhD, Director:

2. Lynn Teesch, PhD, Director of Operations:

3. Idil Apak Evans, PhD, Associate Research Scientist:

4. Reid Brown, PhD, Assistant Research Scientist: 

5. Adam Rauckhorst, PhD, consultant on isotope tracing:

Are you thinking about using metabolomics in your research? We are happy to meet with you to discuss your research and offer advice on the best practices for sample collection and sample submission.

File Download Sample Submission Form

For external price information, please inquire. 

Highlighted Publications

  • Jain A, Kim BR, Yu W, Moninger TO, Karp PH, Wagner BA, Welsh MJ. Mitochondrial uncoupling proteins protect human airway epithelial ciliated cells from oxidative damage. Proc Natl Acad Sci U S A. 2024 Mar 5;121(10):e2318771121. PMID: 38416686; PMCID: PMC10927548. 
  • Rauckhorst AJ, Vasquez Martinez G, Mayoral Andrade G, Wen H, Kim JY, Simoni A, Robles-Planells C, Mapuskar KA, Rastogi P, Steinbach EJ, McCormick ML, Allen BG, Pabla NS, Jackson AR, Coleman MC, Spitz DR, Taylor EB, Zepeda-Orozco D. Tubular mitochondrial pyruvate carrier disruption elicits redox adaptations that protect from acute kidney injury. Mol Metab. 2024 Jan;79:101849. PMID: 38056691; PMCID: PMC10733108. 
  • Li Q, Zhang Q, Kim YR, Gaddam RR, Jacobs JS, Bachschmid MM, Younis T, Zhu Z, Zingman L, London B, Rauckhorst AJ, Taylor EB, Norris AW, Vikram A, Irani K. Deficiency of endothelial sirtuin1 in mice stimulates skeletal muscle insulin sensitivity by modifying the secretome. Nat Commun. 2023 Sep 11;14(1):5595. PMID: 37696839; PMCID: PMC10495425. 
  • Najt CP, Adhikari S, Heden TD, Cui W, Gansemer ER, Rauckhorst AJ, Markowski TW, Higgins L, Kerr EW, Boyum MD, Alvarez J, Brunko S, Mehra D, Puchner EM, Taylor EB, Mashek DG. Organelle interactions compartmentalize hepatic fatty acid trafficking and metabolism. Cell Rep. 2023 May 30;42(5):112435. PMID: 37104088; PMCID: PMC10278152. 
  • Buchanan JL, Tormes Vaquerano J, Taylor EB. Isolated Effects of Plasma Freezing versus Thawing on Metabolite Stability. Metabolites. 2022 Nov 11;12(11):1098. PMID: 36422241; PMCID: PMC9693613. 
  • Rauckhorst AJ, Borcherding N, Pape DJ, Kraus AS, Scerbo DA, Taylor EB. Mouse tissue harvest-induced hypoxia rapidly alters the in vivo metabolome, between-genotype metabolite level differences, and 13C-tracing enrichments. Mol Metab. 2022 Dec;66:101596. PMID: 36100179; PMCID: PMC9589196. 
  • Yonekawa T, Rauckhorst AJ, El-Hattab S, Cuellar MA, Venzke D, Anderson ME, Okuma H, Pewa AD, Taylor EB, Campbell KP. Large1 gene transfer in older myd mice with severe muscular dystrophy restores muscle function and greatly improves survival. Sci Adv. 2022 May 27;8(21):eabn0379. PMID: 35613260; PMCID: PMC9132445. 
  • Fink BD, Rauckhorst AJ, Taylor EB, Yu L, Sivitz WI. Membrane potential-dependent regulation of mitochondrial complex II by oxaloacetate in interscapular brown adipose tissue. FASEB Bioadv. 2021 Dec 3;4(3):197-210. PMID: 35392250; PMCID: PMC8973305. 
  • Jiang J, Reho JJ, Bhattarai S, Cherascu I, Hedberg-Buenz A, Meyer KJ, Tayyari F, Rauckhorst AJ, Guo DF, Morgan DA, Taylor EB, Anderson MG, Drack AV, Rahmouni K. Endothelial BBSome is essential for vascular, metabolic, and retinal functions. Mol Metab. 2021 Nov;53:101308. PMID: 34303879; PMCID: PMC8379702. 
  • Tompkins SC, Sheldon RD, Rauckhorst AJ, Noterman MF, Solst SR, Buchanan JL, Mapuskar KA, Pewa AD, Gray LR, Oonthonpan L, Sharma A, Scerbo DA, Dupuy AJ, Spitz DR, Taylor EB. Disrupting Mitochondrial Pyruvate Uptake Directs Glutamine into the TCA Cycle away from Glutathione Synthesis and Impairs Hepatocellular Tumorigenesis. Cell Rep. 2019 Sep 3;28(10):2608-2619.e6. PMID: 31484072; PMCID: PMC6746334.