Stable Isotope & Metabolomics Core

Services

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 
Acylcarnitines
C0 to C18: 2 
40 species Lipid Fatty acid metabolism 
Glycerophospholipids
C14:0 to C44: 6 
90 species Lipid metabolism Phospholipid biosynthesis 
Sphingolipids
SM C14:1 to SM C26:1 
15 species Lipid metabolism Sphingolipid biosynthesis 
Hexose  5793  Carbohydrate Glycolysis pathwayPentose Phosphate pathway Gluconeogenesis 
 

Back to top 

 

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
Acylcarnitines
C0 to C18:2
41species Lipidmetabolism Fattyacid metabolism
Glycerophospholipids
C6:0 to C44:6
92species LipidMetabolism Phospholipid biosynthesis
Sphingolipids
SM C14:1 to SM C26:1
15sepcies LipidMetabolism Sphingolipid biosynthesis
Hexose 5793 Carbohydrate Glycolysis pathway, Pentose Phosphate pathway , Gluconeogenesis
 

Back to top 

 

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 
 

Back to top 

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 

 

 

 

 

Back to top 

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 6675  Bile Acid Biosynthesis 
Lithocholate 9903  Bile Acid Biosynthesis 
Glycolithocholate 115245  Bile Acid Biosynthesis 
6,7-diketolithocholic acid 21403088  Bile Acid Biosynthesis 
7,12-diketolithocholic acid 22213549  Bile Acid Biosynthesis 
Glycocholate 10140  Bile Acid Biosynthesis 
Glycoursodeoxycholic acid 12310288  Bile Acid Biosynthesis 
Glycodeoxycholate 3035026  Bile Acid Biosynthesis 
Glycochenodeoxycholate 12544  Bile Acid Biosynthesis 
Glycohyodeoxycholate   Bile Acid Biosynthesis 
Taurochenodeoxycholate 387316  Bile Acid Biosynthesis 
Taurohyodeoxycholate 70686868  Bile Acid Biosynthesis 
Taurodeoxycholate 10594  Bile Acid Biosynthesis 
Deoxycholate 222528  Bile Acid Biosynthesis 
Taurolithocholate 439763  Bile Acid Biosynthesis 
Omegamuricohlic acid 5283851  Bile Acid Biosynthesis 
Gamma muricholic 92805  Bile Acid Biosynthesis 
Beta-muricholic acid 5283853  Bile Acid Biosynthesis 
Alpha muricholic acid 53477700  Bile Acid Biosynthesis 
Cholic acid 221493  Bile Acid Biosynthesis 
Tauro-α-muricholic acid    Bile Acid Biosynthesis 
Tauro-β-muricholic acid 168408  Bile Acid Biosynthesis 

References:

  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 

Back to top  

Module #6 Leukotrines and Eicosanoids

BIOCHEMICAL NAME PUBCHEM ID SUPER PATHWAY
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 

Back to top 

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 
                     

Back to top  

Click here to log in