Cancer Metabolism

Investigating the role of metabolism in cancer on both the cellular and organismal level.

Cancer Metabolism Lab Equipment


The Sanford Burnham Prebys Cancer Metabolism Core provides a hub within the Institute for analysis of metabolism using specialist instruments and methodologies, together with advice on planning experiments and analyzing data. All of the instruments and approaches are available on a fee-for-service basis to Cancer Center scientists, but also (as capacity permits) to outside users. Samples for most services can be shipped, but Seahorse analyzer users need to be local so they can bring live cells for analysis.


The primary services offered by the core are:

  • GC/MS-based analysis of metabolites, including:
    1. a panel of 30-40 small polar metabolites (such as amino acids, components of glycolysis and TCA pathways)
    2. fatty acids and cholesterol
    3. sugars and sugar alcohols and acids
    4. sugar phosphates
    5. short-chain fatty acids
  • We do both quantification versus standards and stable isotope (13C, 15N, 2H) tracing, the combination of which can give powerful insights into metabolic activity.
  • Measurement of cellular respiration and glycolysis using Seahorse XFp, XFe24 and XFe96 analyzers. These instruments determine rates of extracellular acidification and oxygen consumption by living cells respectively in a 6-well or larger 24 or 96 well formats. From these data, the relative activity of cellular glycolysis versus oxidative phosphorylation, including the balance of ATP production from these two major energetic processes, may be determined.
  • Measurement of major substrates and metabolites (glucose, glutamine, lactate, and glutamate) in culture medium using the YSI 2950 analyzer. This instrument is able to rapidly (~1 min per metabolite) determine the concentration of these important metabolism substrates from a small volume of sample (100-200 µL). Using a 96-well format, this analysis provides an economical method to roughly define changes in metabolism (e.g., in proliferating versus quiescent cells), and is also useful for checking that cells in culture have a sufficient supply of the major nutrients glucose and glutamine.

Equipment & Resources

  • A Thermo TSQ 9610 GC-MS/MS allows for quantitative analysis of up to 50 common polar metabolites from samples including cells, tumors or serum. Analysis is faster and more unambiguous than with the Shimadzu QP2010.. Development of other methods on the new instrument is ongoing.
  • The YSI 2950 metabolite analyzer is able to measure glucose, glutamine, lactate and glutamate in media in 2-3 minutes for all 4 metabolites in a  96-well format. The minimum volume needed is 100 μl. A full 96-well plate may be analyzed in 3-4 hours and results are typically returned the same or next day.
  • The XFp Analyzer can measure respiration in most cell types, including primary cells, adherent cells, and suspension cells (with attachment). With a 6 well format, the XFp Miniplate is ideal for pairwise comparisons (in triplicate) and the analysis of precious samples, such as patient-derived and other rare samples. We mainly focus on the Cell Mito Stress Test to measure the key parameters of mitochondrial function: basal respiration, ATP production, proton leak, maximal respiration, and spare respiratory capacity. Other protocols to measure the use of alternate substrates or to calculate the relative production of ATP from glycolysis or oxidative phosphorylation are available.
  • The XFe24 Analyzer is similar to the XFp, but well sizes are 2.5x larger and up to 22 samples can be run on one plate. We have available islet capture plates.
  • The XFe96 analyzer has the same well size as the XFp, and can run up to 92 wells on one plate.
  • The Shimadzu QP2010 gas chromatograph-mass spectrometer (GC-MS) is used for broader metabolic analyses including quantification and determination of stable isotope (13C, 15N) labeling rates of intra- and extracellular metabolites, including amino acids, keto and fatty acids, short-chain fatty acids, cholesterol, sugars, and sugar phosphates. Analysis of cells, tissues, tumors, feces, and serum or plasma can be performed. The GC-MS includes chemical ionization options, and sensitive methods using negative chemical ionization are under development.


External resources

  • Scripps LC-MS/MS facility - (Center for Metabolomics and Mass Spectrometry) for broad profiling of metabolites.

Price List

For a complete list of services, please call (858) 646-1000 ext. 3941 or email us.


Cancer Metabolism Services Internal Subsidized Non-Profit For Profit Code
Polar metabolite GCMS quantification per sample $40 $54 $105.20 CMR162
Polar metabolite 13C GCMS analysis per sample $40 $54 $105.20 CMR163
Combined GCMS 13C & quant polar metabolites per sample $70 $94.50 $184.10 CMR170
Fatty acid GCMS analysis quantification, per sample $44 $59.40 $115.72 CMR164
Cholesterol (sterol) GCMS quantification per sample $40 $54 $105.20 CMR165
Fatty acid 13C GCMS analysis per sample $40 $54 $105.20 CMR171
Short-chain fatty acid GCMS quantification per sample $44 $59.40 $115.72 CMR172
Sugars GCMS analysis per sample $40 $54 $105.20 CMR173
Seahorse XFp
(training/ full service)
per plate $200 $270 $526 CMR166
Seahorse XFp
per plate $80 $108 $210.40 CMR168
Seahorse XFe24
(training/ full service)
per plate $300 $405 $789 CMR178
Seahorse XFe24
(self- service)
per plate $190 (Internal only) CMR179
Seahorse XFe96
(training/ full service)
per plate $450 $606.50 $1,183.50 CMR180
Seahorse XFe96
(self- service)
per plate $190 (Internal only) CMR181
YSI metabolite analysis per plate $66 $89.10 $173.58 CMR167
Sample prep – cells per sample $4 $5.40 $10.52 CMR174
Sample prep – medium per sample $2 $2.70 $5.26 CMR175
Sample prep – tumor, tissue, homogenizer use per sample $12 $16.20 $31.56 CMR176



Sample prep charges (CMR174-176) are for sample extraction for GCMS, and are in addition to the GCMS charges. If samples are submitted as dried extracts the prep charges will not apply. See core for details.

Self-service rate for Seahorse analyzers includes the cost of plates, XF-medium and reagents.


Scientific Director
Facility Director


David Scott, Ph.D.
David Scott focuses on the development and application of methods for metabolomics, enhanced by the use of stable isotope substrates. Stable isotopes (mainly 13C) provide an added layer of information to metabolomic studies – not only is static pool information obtained, but it is also possible to infer the origins of metabolites and to track flux through metabolic pathways. Methods used include the analysis of small polar metabolites (mainly amino acids and carboxylic acids) and fatty acids by gas chromatography-mass spectrometry. Other techniques are being developed to analyze and quantify an expanded range of (labeled) metabolites. We have applied these methods in a study of the central carbon metabolism in Escherichia coli, and, in several papers, on melanoma metabolism. Investigations of melanoma cells showed the importance of glutamine metabolism under hypoxia, identified a novel route for the utilization of the carbon backbone of glutamine for fatty acid synthesis, and defined pathways for proline synthesis. Other recent work uses alternately labeled sugars to simultaneously track different inputs to glycans in normal cells and cell lines from patients with glycosylation defects.

Please call (858) 646-3100 ext. 3941 or use the button below to send us an email.

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