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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 Service Core

The mass spectrometry-based Metabolomics Service Core is the hub of the Center’s overall services. The core consists of a central mass spectrometry laboratory and branches to four faculty-guided WCMC advanced service laboratories (Fiehn, Newman, Hammock, Taha) who specialize in specific branches of metabolism. All service requests must use our central ordering platform to receive, log, distribute and report samples and studies.  See the list of all metabolites detected by the WCMC. Please request accurate cost estimates for your specific project from metabolomics@ucdavis.edu

Our Assays and Platforms

Untargeted analyses screen for all detectable compounds using validated chromatography / mass spectrometry methods, and 15-25 internal standards.

Depending on the sample type and platform, 10-30% of all detectable peaks are identified by retention times and mass spectra from MassBank of North America, yielding additional hundreds of structurally unknown compounds for discovery work. Quantitative data are typically reported as relative peak intensities (for example, normalized to the peak intensities found in quality control samples).

Targeted analyses screen only for sets of defined, carefully selected metabolites with high importance in specific biological matrices. Targeted assays perform absolute quantification using sets of stable isotope labeled internal standards. Usually, targeted assays are performed on low abundant compounds that are not detected by discovery-driven untargeted analyses.

Untargeted metabolomic analyses

Primary Metabolism by GC-TOF MS:   $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

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  • 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.

 

Complex Lipids by CSH-QTOF MS/MS: $69 / sample*
order here

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

  • qtof.png
  • For blood plasma, fecal matter, and tissue samples of various origins, normalized relative intensities are reported for up to 450 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!

 

Biogenic amines by HILIC-QTOF MS/MS: $69 / sample*
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covering: acylcarnitines, TMAO, cholines, betaines, SAM, SAH, nucleotides and nucleosides, methylated and acetylated amines, di- and oligopeptides

  • qtof.png
  • For blood plasma, cells, and tissue samples of various origins, normalized relative intensities are reported for up to 150 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

(1) bile acids + steroids   $89-140/sample*
(price is depending on WCMC laboratory involved with different levels of scientific collaboration)

order here

WCMC central service core: combined assay for

Aldosterone, androstanediol, androstenediol, androstenedione, cis-androsterone, cortexolone, cortexone, corticosterone, cortisol, cortisol sulfate, cortisone, Estradiol, 2-methoxyestradiol, estriol, estrone, etiocholanolone, pregnenolone, 17-hydroxypregnenolone, beta-pregnanolone, allo-pregnanolone, Progesterone, 17α-hydroxyprogesterone, dihydroprogesterone, 20-hydroxyprogesterone, testosterone, testosterone glucuronide, dihydrotestosterone, trans-androsterone, dehydroepiandrosterone, dehydroepiandrosterone sulfate

Taurodehydrocholate, Tauro-ω-Muricholic acid, Tauro-α-Muricholic acid, Tauro-β-Muricholic acid, Tauroursodeoxycholic acid, Taurocholic acid, ω-Muricholic acid, Glycoursodeoxycholic acid, Glycohyodeoxycholic acid, α-Muricholic acid, Glycocholic acid, β-Muricholic acid, Taurochenodeoxycholic acid, Taurodeoxycholic acid, Cholic acid, Ursodeoxycholic acid, Glycochenodeoxycholic acid, Glycodeoxycholic acid, Taurolithocholic acid, Chenodeoxycholic acid, Deoxycholic acid, Glycolithocholic acid, Lithocholic acid

(2) oxylipins* $89-140/sample*
(depending on WCMC laboratory involved: different levels of scientific collaboration)

(also called lipoxins, derived from polyunsaturated fatty acids (PUFAs). Oxylipins include thromboxanes and prostaglandins formed by COX enzymes (cyclooxygenases), or hdyroxy-, keto- and epoxy-lipins formed by LOX enzymes (lipoxygenases), or by cytochrome P450 epoxygenase).

order here

WCMC central service core: combined assay for

14,15-DiHETE; 14,15-DiHETrE; 8,15-DiHETE; 15,16-DiHODE; 12,13-DiHODE; 17,18-DiHETE; 9,10-e-DiHO; 11,12-EpETrE; 14,15-EpETrE; 17(18)-EpETE; 11(12)-EpETE; alpha-12(13)-EpODE; alpha-9(10)-EpODE; 14(15)-EpETE; 19(20)-EpDPE; 9,10-EpO; 12(13)Ep-9-KODE; 15,16-EpODE; 8(9)-EpETrE; 9(10)-EpOME; 12(13)-EpOME; 16(17)-EpDPE; 5-KETE; 9-KODE; 15-KETE; 13-KODE; PGF3alpha; Resolvin D1; Lipoxin A4; 9,12,13-TriHOME; 9-Nitrooleate; 10-Nitrooleate; 10-Nitrolinoleate; PGE3; 6-keto-PGF1alpha; 15-deoxy PGJ2; 15-Keto PGE2; PGE1; PGE2; PGD2; PGF2alpha; TXB2

(3) Vitamin D metabolites $89-140/sample*

(price is depending on WCMC laboratory involved with different levels of scientific collaboration)

order here

WCMC central service core: combined assay for

Vitamin D3, Vitamin D2,  25-hydroxyvitamin D2, 25-hydroxyvitamin D3, 3-epi-25-hydroxyvitamin D3, 1α,25-dihydroxyvitamin-D3, 1α,25-dihydroxyvitamin-D2, 24,25-dihydroxyvitamin-D3, and 23,25-dihydroxyvitamin-D3

(4) very short chain fatty acids           $69 / sample*

WCMC central service core: combined assay for acetate, propionate, butyrate and corresponding alcohols. Assay offered for fecal, cecal or intestinal matter but not for plasma.

order here

 

(5) absolute quantification of amino acids in plasma,  $69 / sample

WCMC central service core: combined assay for all proteinogenic amino acids except arginine. The assay uses the EasyFaast quantification kit and GC-MS for 200 ul plasma samples.

order here

 

  • (6) Biocrates AbsoluteIDQ p180 kit :

    $4,960 for a full plate (96 well) for the Biocrates kit itself, plus $44/sample for staff time and consumables

    $3,305 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.

 

    Biocrates AbsoluteIDQ 400 HR kit:

    $5,900 for a full plate (96 well) for the Biocrates kit itself, plus $69/sample for staff time and consumables

    order here

 

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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