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Assays and Services

This is the page for the central service core. We do mass spectrometry for small molecule analysis. This includes metabolomic profiling and targeted analysis.

Metabolomics Central Service Core

The mass spectrometry-based Metabolomics Central Service Core, overseen by laboratory manager Mine Palazoglu, is the hub of the Center’s overall services. At this laboratory, all samples are received, logged, distributed and reports generated. See the list of all target metabolites. Please request accurate cost estimates for your specific project from metabolomics@ucdavis.edu

Our Assays and Platforms

Untargeted analysis on Primary Metabolism:   $69 / sample*
order here
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covering: carbohydrates and sugar phosphates, amino acids, hydroxyl acids, free fatty acids, purines, pyrimidines, aromatics, exposome-derived chemicals

Untargeted Profiling of Primary Metabolism by automatic liner exchange / cold injection GC-TOF mass spectrometry

gctof
  • For blood plasma, urine, fecal matter, and tissue samples of various origins samples, normalized relative intensities are reported for up to 200 identified metabolites in addition to 200-300 compounds of unknown chemical structure.
  • Samples from other sources (tissues, cell cultures) may differ in the number of identified and unidentified compounds.

All metabolites are reported by retention index, quantification mass, biochemical database identifiers and full mass spectra. Metabolites are quantified by peak heights, not in absolute concentrations. However, we can add internal standards and use calibration curves as needed to give absolute (micromolar) concentrations as requested, e.g. for TCA (Krebs cycle) intermediates, glycolysis, pentose phosphate pathway metabolites, amino acids or other targets! Through untargeted analyses, we also detect exposome-type compounds, from microbial conversions of food metabolites to pharmaceutical drugs.

 

Untargeted analysis on Complex Lipids: $69 / sample*
order here

covering: ceramides, sphingomyelins, cholesteryl esters, oxysterols, lyso- and phospholipids, mono-, di- and triacylglycerols, galactosyl- and glucuronyllipids

Untargeted profiling of complex lipids by liquid chromatography Charged Surface Hybrid  CSH-QTOF mass spectrometry

  • qtof.png
  • For blood plasma, fecal matter, and tissue samples of various origins, normalized relative intensities are reported for up to 350 identified lipids in addition to unknowns. Lipids are identified by our mass spectral library of 200,000 MS/MS spectra in addition to accurate masses and retention time matching.
  • Untargeted data processing may add a large number of additional metabolites of unknown chemical structure.
  • Samples from other sources (tissues, urine, cell cultures) may differ in the number of identified and unidentified compounds.
  • All lipids are reported by retention times, quantification masses, biochemical database identifiers and adduct information. Lipids are quantified by peak heights, not in absolute concentrations. However, we are adding 13 internal standards to convert peak heights into good estimates of absolute (micromolar) concentrations for a range of lipid classes typically detected in biofluids and tissues!

 

Untargeted analysis on Biogenic amines: $69 / sample*
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covering: acylcarnitines, TMAO, cholines, betaines, SAM, SAH, nucleotides and nucleosides, methylated and acetylated amines, di- and oligopeptides

Untargeted profiling of biogenic amines by hydrophilic interaction liquid chromatography HILIC-QTOF mass spectrometry

  • qtof.png
  • For blood plasma, cells, and tissue samples of various origins, normalized relative intensities are reported for up to 50 identified biogenic amines in addition to a large list of unknowns. Biogenic amines are identified by matching mass spectra in a targeted library of MS/MS spectra in addition to accurate masses and retention time matching.
  • Untargeted data processing may add a large number of additional metabolites of unknown chemical structure.
  • Samples from other sources (tissues, urine, cell cultures) may differ in the number of identified and unidentified compounds.
  • All biogenic amines are reported by retention times, quantification masses, biochemical database identifiers and adduct information. Biogenic amines are quantified by peak heights, not in absolute concentrations. However, we are adding 9 internal standards to convert peak heights into good estimates of absolute (micromolar) concentrations for a range of biogenic amines typically detected in biofluids and tissues! Through untargeted analyses, we also detect exposome-type compounds, from microbial conversions of food metabolites to pharmaceutical drugs.


Targeted metabolite analyses:

$69 - $140 / sample*
order here

targeting bile acids, steroids, eicosanoids / oxylipins, very short chain fatty acids in different assays

by liquid chromatography-QTRAP or gas chromatography-quadrupole mass spectrometry

  • fluoxetineWe have a range of validated assays for specific compound classes that are not easily captured in the broader untargeted platforms given above. Specifically, steroids and eicosanoids (oxylipins) are very low abundant in most samples and require both internal standards for accurate quantifications and much more labor hours. Hence, these assays are more costly, and require also more volume.

For fecal matter (stool samples) we have validated analyses of very short chain fatty acids (e.g. acetate, propionate and butyrate) and bile acids. We also offer extending these target assays to other matrices, and we offer establishing target methods for hypothesis-driven research and for validation projects following untargeted profiling studies. To the left, you see a calibration curve for fluoxetine concentration in primate plasma. For all targeted assays, data are usually reported in absolute concentrations.

 

 

  • Biocrates AbsoluteIDQ p180 kit :

    $4,500 for a full plate (96 well) for the Biocrates kit itself, plus $44/sample for staff time and consumables

    $2,700 for a half plate for the Biocrates kit itself, plus $44/sample for staff time and consumables

    order here

The kit includes absolute quantification for amino acids and amines. It also includes measurement for 100 lipids and 40 acylcarnitines. Developed specifically for plasma (EDTA/heparin) and serum samples, this uses a 96-well plate and can accommodate either 40 samples (half plate) or 80 samples (full plate) to fit your project needs. If fewer than 80 (resp. 40) samples are submitted, we regret, we still need to charge for the full costs of the Biocrates kit because these cannot be stored and re-used for longer periods of time.

 

For questions regarding metabolomic analysis, please contact: Kelly Paglia metabolomics@ucdavis.edu

For questions regarding NMR, please contact Dr. Bennet Addison, NMR Facility Manager: jbaddison@ucdavis.edu

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