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Please download, complete and email the two Submission forms to appropriate Core staff prior to submission :

Submission Form Sample and Experimental Details Form


The Metabolomics Core provides metabolite profiling analysis to investigators at the University of Utah, the Huntsman Cancer Institute, and outside academic researchers. The Core was originally established 11 years ago as part of the Center of Excellence in Molecular Hematology (NIH 1P30DK072437) and originally provided GC-MS based metabolomics analysis to the hematology community. Since its founding the Core has expanded its capabilities to include LC-MS metabolomics, lipidomics and flux analysis. In short the Core is capable of fully and comprehensively profiling the metabolome.

To maximize the number of metabolites observed the Core is equipped with three chemical analysis platforms, GC-MS, LC-MS and NMR. Please refer to the Services section of the website for further details on the capabilities of each instrument. In addition, protocols for many of our assays are downloadable from this website in PDF form. Core staff will provide additional assay protocols and consultation upon request.


The Metabolomics Core offers 3 types of services; 1) GC-MS based non-targeted metabolomics, 2) LC-MS based non-targeted analysis, and 3) targeted assays. Metabolites observed are dependent upon the concentration found in the sample but a general outline of metabolites are found below.


GC-MS provides an excellent snapshot of central metabolism. It has proven to be highly reliable for the analysis of the metabolites found below.

  1. Amino acids: all but arginine. Cysteine analysis is unreliable due to its free thiol covalently linked to cysteine in proteins.
  2. TCA cycle and related metabolites: lactate, pyruvate, citrate, aconitate, isocitrate, succinate, fumarate, and malate.
  3. Other organic acids: glyoxylatate, ascorbate, 2-isopropylmalate, 2-ketoadipate, 3-methyl-2-oxopentanoate, 4-aminobutyrate, 3-hydroxypyruvate, 4-methyl-2-oxovalerate, cinnamate, citraconate, citramalate, glycerate, mevalonate, and pimelate.
  4. Free fatty acids and sterols: myristate, palmitate, oleate, linoleate, stearate, arachidonate and others.
  5. Glycolytic intermediates: glucose6P, fructose6P, glyceraldehyde3P, dihydroxyacetone phosphate, 1,3-bisphosphoglycerate, 3-phosphoglycerate, 2-phosphoglycerate, and phosphoenolpyruvate.
  6. Carbohydrates: glucose, galactose, mannose, sorbitol, mannitol, xylose, fructose and ribose.
  7. Purine and pyrimidine bases. Adenine, guanine, thymine, cytosine, uracil, orotate, dihydroxyorotate, inosine as well as adenosine, guanosine, uridine and cytidine.


LC-MS provides an excellent platform for the analysis of redox metabolites, nucleotides and lipids.

  1. Redox metabolites: oxidized and reduced glutathione, NADP+, NADPH, NAD+, NADH.
  2. Coenzymes: acetyl-, malonyl-, succinyl-CoA.
  3. Nucleotides: AMP, ADP, ATP, GMP, GDP, GTP and many others.
  4. Lipidomics: Non-targeted lipidomics over 1000 individual lipid species, targeted assays for acyl-carnitines and ceramides routinely performed in the core.

Targeted Assays

The Core has over 600 purchased pure metabolite standards and routinely develops targeted quantitative assays for researchers. These are custom assays, please inquire with the Core for details on feasibility and pricing. Examples of past analysis include:

  1. Hepcidin quantification
  2. Acyl-carnitine quantification
  3. Creatine and phosphocreatine quantification

LC-MS Lipidomic Analysis

The Metabolomics Core offers three types of lipidomics services, 1) LC-MS based non-targeted lipidomics, 2) LC-MS based targeted lipidomics, and 3) GC-MS based fatty acid methyl ester (FAMES) analysis for any biological matrix.

 LC-MS based non-targeted lipidomics

We employ the Agilent 6545 Accurate Mass Q-TOF dual ESI mass spectrometer operating in positive and negative ionization modes coupled with ultra-high performance liquid chromatography (UHPLC) to assay a broad range of lipid classes from any biological matrix. Most often, we examine the lipid differences found between biological samples after perturbation of a given system. While there is no single analytical platform that can fully characterize the highly diverse lipidome, our sample extraction and preparation strategy coupled with reversed-phase HPLC provides a robust tool to assess the lipid content of any biological system. Lipid class coverage includes PC, PE, PG, PI, PS, DAG, TAG, SM, CE, EE, CER, CL, and all related lyso and plasmalogen species. We typically identify >1000 unique lipid species from our untargeted lipidomics platform.

LC-MS based targeted lipidomics

When researchers wish to quantitate specific lipids in a targeted fashion, we employ the Agilent 6490 Triple Quadrupole mass spectrometer and the SCIEX QTRAP 6500 System coupled with UHPLC from any biological matrix. This type of project is often limited to 200 specific lipids from a subset of lipid classes and new assays require method development. We routinely run targeted assays for acylcarnitines and sphingolipids.

GC-MS based fatty acid methyl ester (FAMES) analysis

The metabolomics core utilizes an HP6890 GC-MS interfaced with a flame ionization detector (FID) to analyze FAMEs. Free fatty acids are esterified using acid-catalysis on a variety of biological matrixes.

Biological sample preparation

Sample collection is a vital part of lipid analysis. With the highly sensitive analysis methods available, only a very small amount of source material is needed. Two points should be kept in mind, 1) the small quantity of sample taken should be representative of the entire source material, and 2) just enough material, but not too much, should be sampled for all of the planned analysis. What is enough material? There is no clear answer for this as all source material will vary. Generally, we recommend a minimum of 5 mg of wet tissue, a million of cells, 20 µL of plasma, or 100 µg of protein from a membrane fraction. Too much material would be approximately 20-fold more than the minimum. We also require the researcher to record those values when preparing their samples. With few exceptions, all samples should be flash-frozen, stored under nitrogen if possible and shipped on dry ice. Researchers are free to label their samples as they see fit, although we do recommend a simple labeling scheme that refers back to detailed sample information. If possible, researchers should generate a blank (negative control) sample in their set.

Software and data analysis

LC-MS and tandem MS (MS/MS) data is analyzed using a suite of software packages including Agilent Mass Hunter Qual, Mass Hunter Quant and Profinder. Lipid annotation is provided by our core utilizing existing databases (LipidMaps, METLIN and Lipid Match). Data analysis is conducted using MetaboAnalyst (PCA, volcano plots, heatmaps).


Simcox, Judith et al. Global Analysis of Plasma Lipids Identifies Liver-Derived Acylcarnitines as a Fuel Source for Brown Fat Thermogenesis, Cell Metabolism, Volume 26, Issue 3, 509 – 522.e6


Email Dr. Alan Maschek for information.

2023 Rates

Service CIHD Internal CIHD External University of Utah External Academic Commercial
GC-MS Metabolomics
$39.25 $60.45 $67.25 $103.57 $134.50
LC-MS Metabolomics
$45.09 $69.44 $67.83 $104.46 $135.66
Lipidomics $45.09 $69.44 $79.93 $123.09 $159.86
Senior Associate Data Analysis cost/hour $106.09 $163.38 $103.00 $158.42 $206.00
Associate Data Analysis cost/hour $53.05 $81.69 $53.05 $81.70 $106.10
GC-MS Instrument cost/hour $45.09 $69.44 $43.78 $67.42 $87.56
LC-MS instrument cost/hour $50.92 $78.42 $49.44 $76.14 $98.88

To Place an Order:

Place an Order

Please download, complete and email the two Submission forms to appropriate Core staff prior to submission :

Submission Form Sample and Experimental Details Form


Sample replicates

For quality results, we recommend at least six biological replicates for each experimental condition.


Cell Culture

We recommend 6 million cells minimal for a complete metabolomic analysis, some assays require less (e.g., 1 million for lipidomics). Once cell culture has come to desired confluence, remove media, wash plate with PBS buffer and then remove as much PBS as possible. At this stage, you have several options.

Option 1 – Preferred) If you can remove the cells from the plate by trypsin or other method, transfer the cell culture to a microfuge tube, pellet by centrifugation then remove as much supernatant as possible. Snap freeze on dry ice, flush with nitrogen gas and send us the sample via FedEx on dry ice. We will add several internal standards to the extraction for data normalization.

Option 2) Extract the cells yourself. After PBS, add 1 mL of cold 80% MeOH solution to the plate, scrape cells into a microfuge tube, vortex and incubate for 1 hour at -20 °C. Centrifuge at max speed for 5 minutes at 4 °C. Remove supernatant, transfer to new tube and dry supernatant in a speedvac or under gentle nitrogen stream. Send us the samples in freezer box with small desiccant bags added.


Plasma/Serum Preparation

Collect serum or plasma per usual, but do not use sodium citrate in the preparation of samples as this strongly affects the results. Once you have serum collected snap freeze 20-50 µL of it for metabolomics analysis and deliver to the Core. This is the preferred method of sample submission. If you wish to extract the metabolites from serum/plasma, please follow these instructions. To 50 µL of serum, add 450 µL of cold 90% methanol and vortex for 10 seconds followed by 1 hour incubation at -20 °C.  Centrifuge the mixture at 14,000 rpm for 5 min at 4˚C to precipitate the protein, transfer to new tube and dry supernatant in a speedvac or under gentle nitrogen stream. Perform the extraction on ice or in an -20 °C type enzyme caddy.


Yeast Preparation

For a single GC-MS or LC-MS analysis, five total ODs of cells are required. For example, cells harvested at a 1 OD, 5 mL of this culture will be needed. For metabolite profiling pellet 5 OD’s of cells in a 15 mL conical tube, remove supernatant, snap freeze and deliver samples to the Core. This is the preferred method. If you wish to extract the cultures, please follow this procedure. Prepare and 75% EtOH solution and warm in a water bath to 80 °C. Once hot, add 5 mL of this solution to each sample in a 15 mL tube, vortex vigorously and incubate in the hot water bath for 5 minutes. Pellet the cell via centrifuge, transfer to new tube and dry supernatant in a speedvac or under gentle nitrogen stream.


Tissue Preparation

Analysis of tissue can be highly variable, for complete metabolic analysis we recommend a minimum of 20 mg of wet tissue. Tissues samples should be representative of the entire tissue, snap frozen and stored under nitrogen if possible. Researchers are required to record the masses of the tissue when preparing their samples. We prefer to extract all tissue samples in the Core laboratory using a high-speed bead mill for this. Tissue preparation is sample dependent; please contact the Director for a discussion on methods.

James Cox

15 N Medical Drive East

Bldg 565 Room A306

Salt Lake City UT 84112


Hours of Operation

Monday-Friday 9am-5pm


Emma Eccles Jones Medical Science Building (EEJ) Room A306
15 N Medical Dr East
Salt Lake City, UT 84112

Access is through the North or South stairwell as well as the service elevator.


James Cox, Ph.D. , Director
Phone: 801-587-7779
Fax: 801-585-6362

Alan Mashchek, Ph.D.

Leon Catrow, Ph.D.

Sandra Osburn, Ph.D.

Quentinn Pearce, Ph.D.


Austin Taylor, Lab Technician

Oversight Committee

Jared Rutter
Dennis Winge
Eric Schmidt
Carl Thummel

Acknowledgement Guidelines for the Metabolomics Core

We recognize three levels of acknowledgement for core contributions to a publication.

  1. If simple fee for service data generation was performed with no intellectual input from core staff, then please recognize the core in the Acknowledgement section of the publication as follows, “Metabolomics analysis was performed by the Metabolomics Core at the University of Utah Health Sciences Centers using equipment provided for by University of Utah RIF funds.”
  2. If effort beyond normal fee for service work was performed by core staff but little to no intellectual contribution was made, please acknowledge the core and the staff member that performed the analysis as follows, “Metabolomics analysis was performed by “Core Staff Member” in the Metabolomics Core at the University of Utah School of Medicine Centers using equipment provided for by University of Utah RIF funds.
  3. If an intellectual contribution has been made by Metabolomics Core staff that is included in the publication then authorship is warranted. In addition, in the Acknowledgement section of a publication recognize the core as follows, “Metabolomics analysis was performed by the Metabolomics Core at the University of Utah School of Medicine Centers using equipment provided for by University of Utah RIF funds.

The Metabolomics Core processes every sample using two distinct but overlapping procedures, a targeted analysis and a non-targeted analysis. The targeted analysis is used to search every chromatogram for known metabolites in which the Core has purchased a standard  for and is highly confident in its identitiy. We use instrument specific software to report the area under the curve for each of these known metabolites and transfer this data to an Excel spreadsheet. We then perform a non-targeted analysis in which data mining software just detects chromatographic peaks that are altered in two different conditions. This is normally done by Priniciple Components Analysis (PCA) and Partial Least Squares-Discriminate Analysis (PLS-DA). Many times this detects known compounds but in the case where an unknown compound is found to be altered we add this to the Excel spreadsheet using a unique identifier. It is identified by its chromatographic retention time (rt) and a charecteristic mass (m/z) in the form of unrt_m/z. For example if an unkown was found at retention time of 10.78 minutes and had a mass of 347.0111 it would be labeled as un10.78_347.

The Core then uses the data generated in these two procedures for further basic analysis using a number of statistical packages including The Core highly recomends users to visit this website and to further examine their data. The Core will provide users with a final report outling the experimental procedures performed and basic statistics analysis. Attached with this report is all the raw data so each user can further examine the results. Metabolomics related resources are listed in the Online Resorces tab.


Agilent 6545 LC-MS QTOF (two instruments)

Two Agilent 6545 UPLC-QToF mass spectrometers are used for non-targeted lipidomics and LC-MS metabolomics. Ultra-pressure reversed phase liquid (UPLC) chromatography is employed for lipid separation prior to analysis. Hydrophilic interaction liquid chromatography (HILIC) is used for separation of polar metabolites such as nucleotides and redox metabolites.

Agilent 6490 LC-MS QQQ

An Agilent 6490 Triple Quadrupole (QQQ) mass spectrometer coupled to an Agilent 1290 UPLC is used as our primary instrument for the targeted quantification of lipids including sphingolipids and carnitines. UPLC is employed for rapid chromatographic fractionation prior to analysis.


A SCIEX 6500 QTRAP mass spectrometer coupled to a SCIEX NEXERA UPLC is used as our primary instrument for the targeted quantification of polar metabolites and drug molecules. Ultra-pressure reversed phase liquid chromatography and HILIC are utilized as necessary for separation of metabolites prior to quantification.

Agilent 7200 GC-QTOF with EI and CI capabilities

This state of the art gas chromatograph-mass spectrometer is a high resolution/high mass accuracy quadrupole time-of-flight instrument. It is fitted with an Agilent 7693 auto sampler that automates sample preparation for high throughput sample analysis. This workhorse instrument is primary used for the analysis of the low molecular weight metabolome and for flux analysis.

Agilent 5977b with High Efficiency Source

The Core has two Agilent 5977b  single quadrupole GC-MS systems.  These use a High Efficiency Source that increases the number of ions that reach the detector.  This greatly increases instrument sensitivity.  Fit with an Agilent 7693 autosampler, this instrument is consistent and easy to maintain. These instruments are used to perform low molecular weight metabolomics and isotope tracer analysis.



Representative Metabolomics Core Publications:

Isotope Tracing: Marcero JR, Cox JE, Bergonia HA, Medlock AE, Phillips JD, Dailey HA. The immunometabolite itaconate inhibits heme synthesis and remodels cellular metabolism in erythroid precursors. Blood Adv. 2021 Dec 14;5(23):4831-4841. doi: 10.1182/bloodadvances.2021004750. PubMed PMID: 34492704.

Isotope Tracing: Burch JS, Marcero JR, Maschek JA, Cox JE, Jackson LK, Medlock AE, Phillips JD, Dailey HA Jr. Glutamine via α-ketoglutarate dehydrogenase provides succinyl-CoA for heme synthesis during erythropoiesis. Blood. 2018 Sep 6;132(10):987-998. doi: 10.1182/blood-2018-01-829036. Epub 2018 Jul 10. PubMed PMID: 29991557; PubMed Central PMCID: PMC6128084.

Lipidomics: Jadhav S, Protchenko O, Li F, Baratz E, Shakoury-Elizeh M, Maschek A, Cox J, Philpott CC. Mitochondrial dysfunction in mouse livers depleted of iron chaperone PCBP1. Free Radic Biol Med. 2021 Nov 1;175:18-27. doi: 10.1016/j.freeradbiomed.2021.08.232. Epub 2021 Aug 26. PubMed PMID: 34455040.

Metabolomics: Schuler MH, English AM, Xiao T, Campbell TJ, Shaw JM, Hughes AL. Mitochondrial-derived compartments facilitate cellular adaptation to amino acid stress. Mol Cell. 2021 Sep 16;81(18):3786-3802.e13. doi: 10.1016/j.molcel.2021.08.021. PubMed PMID: 34547239; PubMed Central PMCID: PMC8513802.

All Modalities: Simcox J, Geoghegan G, Maschek JA, Bensard CL, Pasquali M, Miao R, Lee S, Jiang L, Huck I, Kershaw EE, Donato AJ, Apte U, Longo N, Rutter J, Schreiber R, Zechner R, Cox J, Villanueva CJ. Global Analysis of Plasma Lipids Identifies Liver-Derived Acylcarnitines as a Fuel Source for Brown Fat Thermogenesis. Cell Metab. 2017 Sep 5;26(3):509-522.e6. doi: 10.1016/j.cmet.2017.08.006. PubMed PMID: 28877455; PubMed Central PMCID: PMC5658052.