West Coast Metabolomics Center - Assays and Services

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) that 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 This email address is being protected from spambots. You need JavaScript enabled to view it..

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.

*per-sample rates below are estimates for 500 samples. Actual-per sample rate will vary depending on how many samples are submitted and substantially increase for small sample sets.

Costs for all assays include sample preparation, data acquisition, data processing, and data curation.
Data results are given as *.csv files. Raw data files are submitted based on request.

Rates comprise data acquisition (by platform) as well as hourly rates for services rendered by staff for sample preparation, data processing, data curation, and reporting. These are estimates and the per-sample prices changes with the number of samples that are submitted. For a study of 500 samples and using all three non-targeted assays combined (two LC-accurate mass MS/MS with positive/negative ESI injections, plus GC-TOF MS), per-sample rates in 2022 are $154 for clients from University of California, $240 for non-UC academic institutions and $297 for industry. For individual assays on 500 samples, see below.

Primary Metabolism by GC-TOF MS:
carbohydrates and sugar phosphates, amino acids, hydroxyl acids, free fatty acids, purines, pyrimidines, aromatics, exposome-derived chemicals

$81 / sample ($52 for UC clients) order here

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 BEH C18-QTOF MS/MS:
ceramides, sphingomyelins, cholesteryl esters, lyso- and phospholipids, mono-, di- and triacylglycerols, galactosyl- and glucuronyllipids

$114 / sample ($73 for UC clients) order here

For blood plasma, fecal matter, and tissue samples of various origins, normalized relative intensities are reported for up to 550 identified lipids in addition to unknowns. Lipids are identified by our mass spectral library of 400,000 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:
acylcarnitines, TMAO, cholines, betaines, SAM, SAH, nucleotides and nucleosides, methylated and acetylated amines, di- and oligopeptides

$114 / sample ($73 for UC clients) order here

For blood plasma, cells, and tissue samples of various origins, normalized relative intensities are reported for up to 300 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.

Polyphenols and flavonoids by BEH C18-Q Exactive MS/MS:
flavonoids, anthocyanins, polyphenols, di- and triterpenes, sesquiterpenes, coumarins, terpene- and polyphenol-glycosides, kaempferols, flavanons, cinnamates, and related compounds.

$114 / sample ($73 for UC clients) order here

For plant, food and gut intestinal/fecal matter samples of various origins, normalized relative intensities are reported for up to 400 identified polyphenols and natural products in addition to a large list of unknowns. These compounds 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.
All polyphenols and natural products are reported by retention times, quantification masses, biochemical database identifiers and adduct information. These natural products are quantified by peak heights, not in absolute concentrations. However, we are adding 10 internal standards to convert peak heights into good estimates of absolute (micromolar) concentrations for a range of polyphenols typically detected in foods or plant tissues! Through untargeted analyses in urine, we may also detect exposome-type compounds, from polyaromatic hydrocarbons to PCBs, using glucuronidase in sample pre-treatment.

Targeted metabolite analyses

$93 / sample ($59 for UC clients) order here

Bile acids

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

Steroids

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

Oxylipins

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

Very short-chain fatty acids

acetate, propionate, butyrate, and corresponding alcohols. Assay offered for fecal, cecal, or intestinal matter but currently not for plasma.
If you need this assay for plasma, please check back with us. The assay may be finalized for validation in 06/2023.

Stable isotope tracer analysis

Through funding by UC Davis, the WCMC now offers isotope tracer analysis for studies such as metabolic reprogramming in cancer cells, but also for flux studies in bacteria or yeasts, for pharmacological studies or environmental studies where stable isotope tracers might be needed.

Assays and Services

Our Assays and Platforms

Primary Metabolism by GC-TOF MS: carbohydrates and sugar phosphates, amino acids, hydroxyl acids, free fatty acids, purines, pyrimidines, aromatics, exposome-derived chemicals

$81 / sample ($52 for UC clients) order here

Complex Lipids by BEH C18-QTOF MS/MS: ceramides, sphingomyelins, cholesteryl esters, lyso- and phospholipids, mono-, di- and triacylglycerols, galactosyl- and glucuronyllipids

$114 / sample ($73 for UC clients) order here

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

$114 / sample ($73 for UC clients) order here

Polyphenols and flavonoids by BEH C18-Q Exactive MS/MS: flavonoids, anthocyanins, polyphenols, di- and triterpenes, sesquiterpenes, coumarins, terpene- and polyphenol-glycosides, kaempferols, flavanons, cinnamates, and related compounds.

$114 / sample ($73 for UC clients) order here

Targeted metabolite analyses

Bile acids

Steroids

Oxylipins

Very short-chain fatty acids

Stable isotope tracer analysis

Primary Metabolism by GC-TOF MS:
carbohydrates and sugar phosphates, amino acids, hydroxyl acids, free fatty acids, purines, pyrimidines, aromatics, exposome-derived chemicals

Complex Lipids by BEH C18-QTOF MS/MS:
ceramides, sphingomyelins, cholesteryl esters, lyso- and phospholipids, mono-, di- and triacylglycerols, galactosyl- and glucuronyllipids

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

Polyphenols and flavonoids by BEH C18-Q Exactive MS/MS:
flavonoids, anthocyanins, polyphenols, di- and triterpenes, sesquiterpenes, coumarins, terpene- and polyphenol-glycosides, kaempferols, flavanons, cinnamates, and related compounds.