Stable Isotope & Metabolomics Core


Before bringing samples , please fill out the order form ,sample manifesto and E-mail to Hardik Shah, so we can give you an estimate for the services needed. You will have to provide a grant number to be charged for these services, you will not be charged until you receive your data. The order form, sample manifest form, and sample manifest guidelines can be downloaded using the window highlighted to the right of this introduction. Please bring the sample manifest along with the samples. You must review the markings on all tubes/samples so when a bar code is generated for your samples, there will be no confusion.

For the modules listed below, information is organized for your review of the pertinent metabolic pathways. For example in module 1 there are “hyperlinks” in the Pubchem ID and subpathway columns. If you click the hotlink in pubchem, it will take you to pages of information about the metabolite, including structures. If you click on the subpathway hyperlink, you will get taken to the small molecule pathway diagram database, and you can visualize where your metabolite is relative to others in the pathway. Clicking on a metabolite in the figure will take you to the human metabolome database for more specific information about that metabolite.

Module #1 180 Metabolites 

The targeted metabolomics approach in this assay is based on measurements with the AbsoluteIDQ p180 kit (BIOCRATES Life Sciences AG, Innsbruck, Austria). This method allows simultaneous quantification of 188 metabolites using liquid chromatography and flow injection analysis–mass spectrometry. For an example of this Module’s utility, see Wang-Sattler et al Novel biomarkers for pre-diabetes identified by metabolomics, Molecular Systems Biology 8; 615; doi:10.1038/msb.2012.43

Biochemical Name Pubchem ID Super Pathway Sub Pathway
Alanine  5950  Amino acids  Alanine metabolism,Aspartate metabolism 
Arginine  3362  Amino acids  Urea cycle, Arginine and Proline metabolism 
Asparagine  6267  Amino acids  Aspartate metabolism 
Aspartic acid  5960  Amino acids  Aspartate metabolism 
Citrulline  9750  Amino acids  Urea cycle 
Glutamine  5961  Amino acids  Glutamate metabolism 
Glutamic Acid  33032  Amino acids  Glutamate metabolism 
Glycine  750  Amino acids  Glycine and serine metabolism 
Histidine  6274  Amino acids  Histidine metabolism 
Isoleucine  6306  Amino acids  Valine, Leucine and Isoleucine Degradation 
Leucine  6106  Amino acids  Valine, Leucine and Isoleucine Degradation 
Lysine  5962  Amino acids  Lysine Degradation 
Methionine  6137  Amino acids  Methionine metabolism 
Ornithine  6262  Amino acids  Urea cycleArginine and Proline metabolism 
Phenylalanine  6140  Amino acids  Phenylalanine and Tyrosine metabolism 
Proline  145742  Amino acids  Arginine and Proline metabolism 
Serine  5951  Amino acids  Glycine and serine metabolism 
Threonine  6288  Amino acids  Threonine and 2-oxobutanoate degradation 
Tryptophan  6305  Amino acids  Tryptophan metabolism 
Tyrosine  6057  Amino acids  Phenylalanine and Tyrosine metabolism 
Valine  6287  Amino acids  Valine,Leucine and Isoleucine metabolism 
Acetylornithine  439232  Amino acids  Arginine and proline metabolism 
Asymmetric dimetylarginine  123831  Amino acids Not Available
alpha-Aminoadipic acid  469  Amino acids  Lysine Degradation 
Carnosine  439224  Amino acids  beta-Alanine metabolism, Histidine metabolism 
Creatinine  588  Amino acids  Creatinine 
Dopa  6047  Amino acids  Catecholamine Biosynthesis 
Dopamine  681  Amino acids  Catecholamine biosynthesis 
Histamine  774  Amino acids  Histidine metabolism 
Kynurenine  161166  Amino acids  Tryptophan Degradation,Lysine Degradation 
Methioninesulfoxide  847  Amino acids  Methionine metabolism 
Nitrotyrosine  65124  Amino acids  Phenylalanine and Tyrosine metabolism 
Hydroxyproline  5810  Amino acids  Arginine and Proline metabolism 
Phenylethylamine  1001  Amino acids  Tyrosine metabolism 
Putrescine  1045  Amino acids  Spermidine and Spermine biosynthesis 
Sacrcosine  1088  Amino acids  Glycine and Serine metabolism 
Symmetric dimethylarginine  169148  Amino acids  Urea cycleArginine and Proline metabolism 
Serotonin  5202  Amino acids  Tryptophan metabolism 
Spermidine  1102  Amino acids  Spermidine and Spermine biosynthesis 
Spermine  1103  Amino acids  Spermidine and Spermine biosynthesis 
Taurine  1123  Amino acids  Taurine and Hypotaurine metabolism 
Total dimethylarginine  123831  Amino acids  Arginine and Proline metabolism 
C0 to C18: 2 
40 species Lipid  Fatty acid metabolism 
C14:0 to C44: 6 
90 species Lipid metabolism  Phospholipid biosynthesis 
SM C14:1 to SM C26:1 
15 species Lipid metabolism  Sphingolipid biosynthesis 
 Hexose   5793  Carbohydrate  Glycolysis pathwayPentose Phosphate pathway Gluconeogenesis 



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Module #2-150 Metabolites

The targeted metabolomics approach in this assay is based on measurements with the AbsoluteIDQ p150 kit (BIOCRATES Life Sciences AG, Innsbruck, Austria). This method allows simultaneous quantification of 150 metabolites using flow injection analysis–mass spectrometry. This module can be calibrated for use with urine metabolites, as well as plasma. For an example of its use with plasma measurements, see Solberg et al Metabolomic Analyses of Plasma Reveals New Insights into Asphyxia and Resuscitation in Pigs PLoS ONE 5(3): e9606. doi:10.1371/journal.pone.0009606.

Biochemical Name Pubchem ID Super Pathway Sub Pathway
Arginine 3362 Aminoacids Urea cycle, Arginine, Proline metabolism
Glutamine 5961 Aminoacids Glutamate metabolism
Glycine 750 Aminoacids Glycine,Serine,Threonine metabolism
Histidine 6274 Aminoacids Histidine metabolism
Isoleucine/leucine 6306 Aminoacids Valine,Leucine, Isoleucine metabolism
Methionine 6137 Aminoacids Cycteine,Methionine, SAM, Taurine metabolism
Ornithine 6262 Aminoacids Urea cycle, Arginine, Proline metabolism
Phenylalanine 6140 Aminoacids Tyrosine metabolism
Proline 145742 Aminoacids Urea cycle, Arginine, Proline metabolism
Serine 5951 Aminoacids Glycine,Serine,Threonine metabolism
Threonine 6288 Aminoacids Glycine,Serine, Threonine metabolism
Tryptophan 6305 Aminoacids Tryptophan metabolism
Tyrosine 6057 Aminoacids Phenylalanine & Tyrosine metabolism
Valine 6287 Aminoacids Valine,Leucine,Isoleucine metabolism
C0 to C18:2
41species Lipidmetabolism Fattyacid metabolism
C6:0 to C44:6
92species LipidMetabolism Phospholipid biosynthesis
SM C14:1 to SM C26:1
15sepcies LipidMetabolism Sphingolipid biosynthesis
Hexose 5793 Carbohydrate Glycolysis pathway, Pentose Phosphate pathway , Gluconeogenesis



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Module #3 Glycolysis, Pentose Phosphate and TCA Metabolites   



Biochemical Name Pubchem ID Super Pathway Sub Pathway
Fructose-1,6-bisphosphate  445555  Carbohydrates  Glycolysis pathway  
6-phospho-D-gluconate  91493  Carbohydrates  Pentose Phosphate pathway  
Glucosamine-6-phosphate  439217  Carbohydrates  Amino sugar metabolism  
3-phosphoglycerate  724  Carbohydrates  Glycolysis, Gluconeogenesis 
Glucose-6-phosphate  5958  Carbohydrates  GlycolysisGluconeogenesis 
Ribose-5-phosphate  439167  Carbohydrates  Pentose Phosphate pathway 
Uridine diphosphate glucose  53477679  Carbohydrates  Nucleotide sugars metabolism  
N-acetyl glucosamine  440996  Carbohydrates  Amino sugar metabolism  
alpha-glycerol-3-phosphate  439162  Carbohydrates  Glycolysis pathway 
Phosphoenolpyruvate  1005  Carbohydrates  GlycolysisGluconeogenesispyruvate metabolism 
alpha ketoglutaric acid  51  Carbohydrates  Krebs Cycle 
Aspartic acid  5960  Carbohydrates  Aspartate Metabolism, Urea Cycle  
citric acid  311  Carbohydrates  Krebs Cycle 
Succinic acid  1110  Carbohydrates  Krebs Cycle 
fumaric acid  444972  Carbohydrates  Krebs Cycle 
Pyruvic acid  1060  Carbohydrates  GlycolysisGluconeogenesispyruvate metabolism 
Lactic acid  107689  Carbohydrates  GlycolysisGluconeogenesispyruvate metabolism 



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Module #4 Redox and Bioenergetics

Biochemical Name Pubchem ID Super Pathway Sub Pathway
ATP  5957  Carbohydrates  Glycolysis pathway, Krebs Cycle  
ADP  6022  Carbohydrates  Glycolysis pathwayKrebs Cycle  
AMP  41211  Carbohydrates  Glycolysis pathwayKrebs Cycle  
NAD  5893  Carbohydrates  Nicotinate and Nicotinamide metabolism 
NADH  928  Carbohydrates  Nicotinate and Nicotinamide metabolism 
NADP  5886  Carbohydrates  Nicotinate and Nicotinamide metabolism 
NADPH  22833512  Carbohydrates  Nicotinate and Nicotinamide metabolism 

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Module #5 Bile Acids

 bile acids assay 

Bile acids are synthesized from cholesterol through both classical and alternative pathways. In the alternative pathway, the side chain oxidation of cholesterol precedes the steroid ring modifications, first yielding 24-, 25-, and 27-hydroxycholesterol metabolites, opposite to the process in the classical pathway. The alternative and classical pathway bile acids share the primary bile acid chenodeoxycholic acid, with 12-α-hydroxylation of chenodeoxycholic acid via CYP8B1to cholic acid. Modifications of bile acids can affect their properties and their ability to activate bile acid receptors. Dysregulation of bile acid synthesis can be seen in inborn errors of metabolism, insulin resistance, hepatocellular Ca and chronic ethanol consumption. Perturbations in the microbiome also affect bile acid pool size and composition (see references below). This panel surveys conditions of bile acid dysregulation.

Metabolite Name  Pubchem/Chemspider ID Pathway
Taurocholic acid (TCA)  6675   Bile Acid Biosynthesis 
Lithocholate (LCA)  9903   Bile Acid Biosynthesis 
Glycolithocholate (GLCA)  115245   Bile Acid Biosynthesis 
6,7-diketolithocholic acid  21403088   Bile Acid Biosynthesis 
7,12-diketolithocholic acid  22213549   Bile Acid Biosynthesis 
Glycocholate (GCA)  10140   Bile Acid Biosynthesis 
Glycoursodeoxycholic acid (GUDCA)  12310288   Bile Acid Biosynthesis 
Glycodeoxycholate (GDCA)  3035026   Bile Acid Biosynthesis 
Glycochenodeoxycholate (GCDCA)  12544   Bile Acid Biosynthesis 
Glycohyodeoxycholate (GHDCA)    Bile Acid Biosynthesis 
Taurochenodeoxycholate (TCDCA)  387316   Bile Acid Biosynthesis 
Taurohyodeoxycholate (THDCA)  70686868   Bile Acid Biosynthesis 
Taurodeoxycholate (TDCA)  10594   Bile Acid Biosynthesis 
Deoxycholate (DCA)  222528   Bile Acid Biosynthesis 
Taurolithocholate (TLCA)  439763   Bile Acid Biosynthesis 
Omegamuricohlic acid (Ω-MCA)


 5283851   Bile Acid Biosynthesis 
Gamma muricholic acid (Γ-MCA)


 92805   Bile Acid Biosynthesis 
Beta-muricholic acid (β-MCA)  5283853   Bile Acid Biosynthesis 
Alpha muricholic acid (α-MCA)  53477700   Bile Acid Biosynthesis 
Cholic acid (CA)  221493   Bile Acid Biosynthesis 
Tauro-α-muricholic acid (Tα-MCA)    Bile Acid Biosynthesis 
Tauro-β-muricholic acid (Tβ-MCA)  168408   Bile Acid Biosynthesis 


  1. More detailed pathways see Bile acid Biosynthesis, Primary Bile acid Biosynthesis, Secondary Bile acid Biosynthesis 
  2.  Human insulin resistance is associated with increased plasma levels of 12α-hydroxylated bile acids Haeusler RA, Astiarraga B, Camastra S, Accili D, Ferrannini E. Diabetes. 2013 Dec; 62(12):4184-91. doi: 10.2337/db13-0639. Epub 2013 Jul 24 
  3.  Application of combined omics platforms to accelerate biomedical discovery in diabesity.Kurland IJ, Accili D, Burant C, Fischer SM, Kahn BB, Newgard CB, Ramagiri S, Ronnett GV, Ryals JA, Sanders M, Shambaugh J, Shockcor J, Gross SS. Ann N Y Acad Sci. 2013 May;1287:1-16. doi: 10.1111/nyas.12116. Epub 2013 May 9. 
  4.  Serum and urine metabolite profiling reveals potential biomarkers of human hepatocellular carcinoma. Chen T, Xie G, Wang X, Fan J, Qiu Y, Zheng X, Qi X, Cao Y, Su M, Wang X, Xu LX, Yen Y, Liu P, Jia W. Mol Cell Proteomics. 2011 Jul; 10(7):M110.004945. doi: 10.1074/mcp.M110.004945. Epub 2011 Apr 25. Erratum in: Mol Cell Proteomics. 2011 Nov; 10(11). doi:10.1074/mcp.A110.004945. 
  5.  Alteration of bileacid metabolism in the rat induced by chronic ethanol consumption.Xie G, Zhong W, Li H, Li Q, Qiu Y, Zheng X, Chen H, Zhao X, Zhang S, Zhou Z, Zeisel SH, Jia W. FASEB J. 2013 Sep;27(9):3583-93. doi: 10.1096/fj.13-231860. Epub 2013 May 24. 
  6.  Bile acidsand the gut microbiome. Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS.Curr Opin Gastroenterol. 2014 May;30(3):332-8 

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Module #6 Leukotrines and Eicosanoids

5(S)-HETE  5280733   Arachidonic Acid Metabolism 
12(S)-HETE  5312983   Arachidonic Acid Metabolism 
15(S)-HETE  5280724   Arachidonic Acid Metabolism 
Leukotriene-E4  5280749   Arachidonic Acid Metabolism 
Leukotriene-B4  5280492   Arachidonic Acid Metabolism 

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Module #7  GC/MS Small Metabolite Screen

Detailed website information under development 

GC/MS will identify at least 40 to 50 small metabolites, in the combined glycolytic/gluconeogenic, pentose and TCA cycle pathways. For an example by the SIMC facility, see Vaitheesvaran B, Yang L, Hartil K, Glaser S, Yazulla S, et al. (2012) Peripheral Effects of FAAH Deficiency on Fuel and Energy Homeostasis: Role of Dysregulated Lysine Acetylation. PLoS ONE 7(3): e33717. doi:10.1371/journal.pone.0033717

Module #8 GC-FID Fatty Acid Profiling

Detailed website information under development


Module #9  Lipogenesis by Deuterated water

Detailed website information under development

Both fatty acid and cholesterol synthesis can be assessed in tissues, depending on the time frame for the study. For examples by the SIMC Facility see Haas et al, Hepatic Insulin Signaling Is Required for Obesity-Dependent Expression of SREBP-1c mRNA but Not for Feeding-Dependent Expression, Cell Metabolism 15, 873–884, 2012; Zhao et al Regulation of lipogenesis by cyclin-dependent kinase 8–mediated control of SREBP-1, J. Clin. Invest. 122:2417-27, 2012; Vaitheesvaran B, Yang L, Hartil K, Glaser S, Yazulla S, et al. (2012) Peripheral Effects of FAAH Deficiency on Fuel and Energy Homeostasis: Role of Dysregulated Lysine Acetylation. PLoS ONE 7(3): e33717 

Module #10 Protein Synthesis by Deuterated Water

Detailed website information under development

Module #11 HGP U13C Glucose Osmotic Mini-Pump

Detailed website information under development

Module #12 Hepatic Recycling Glucose Tolerance Test

Illustrative diagram of pathways for hepatic metabolism of the deuterium-labeled [2-2H1]/[6,6-2H2]glucose. Use of deutrated, instead of unlabeled glucose during a GTT allows for the estimation of hepatic and peripheral glucose disposal. Equal amounts of D1 and D2 glucose ( [2-2H1]- and [6,6-2H2] glucose) are given, at 1 mg glucose/gm body weight. De-deuteration of [2-2H1] glucose occurs during the equilibration of glucose-6-P (G-6-P) with fructose-6-P (F-6-P), which causes plasma D1/D2 levels to decrease. De-deuteration of [6,6-2H1]glucose does not occur until the deuterated glucose reaches the level of pyruvate.  Whole body glucose disposal (mainly peripheral) is reflected in the area under the curve of [6,6-2H2] glucose  during the GTT. Hepatic vs peripheral glucose disposal can be assessed from the differences in plasma [2-2H1]- and [6,6-2H2] glucose during the GTT. This test allows for non-invasive monitoring of peripheral and hepatic glucose disposal, and the mice can be used, after recovery, for additional phenotyping tests.  GK, glucokinase; G6Pase, glucose-6-phosphatase; PK, pyruvate kinase. Diagram from Xu et al Decreased Hepatic Futile Cycling Compensates for Increased Glucose Disposal in the Pten Heterodeficient Mouse, Diabetes 55: 3372-3380, 2006. More examples, done by the SIMC Facility: Vaitheesvaran, LeRoith and Kurland MKR mice have increased dynamic glucose disposal despite metabolic inflexibility, and hepatic and peripheral insulin insensitivity Diabetologia 53:2224–2232, 2010; Vaitheesvaran et al Advantages of dynamic ‘‘closed loop’’ stable isotope flux phenotyping over static ‘‘open loop’’ clamps in detecting silent genetic and dietary phenotypes Metabolomics 6:180–190, 2010; Zong et al Enhanced Energy Expenditure, Glucose Utilization, and Insulin Sensitivity in VAMP8 Null Mice Diabetes. 60: 30–38, 2011

  Module10 diagram  

Module #13 Endocannabinoids-anandamide

  Under development 

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