Metabolome & Lipidome Analyses

Single pathway targeted analyses (absolute quantification) | Multiple pathway targeted analyses (relative quantification) | Targeted lipidomics (absolute quantification) | Stable isotope-assisted analyses | Untargeted analyses
 

Single pathway targeted analyses (absolute quantification)

Amino acid metabolism
alanine glutamate ornithine
alpha-aminoadipate glutamine phenylalanine
alpha-aminobutyrate glycine pipecolate
anserine guanidinoacetate proline
arginine histidine serine
asparagine homocitrulline taurine
beta-alanine/sarcosine isoleucine threonine
carnosine kynurenine trans-4-hydroxy-proline
citrulline leucine tryptophan
creatine lysine tyrosine
gamma-aminobutyrate methionine valine
Acylcarnitine metabolism
Carnitine
Acetylcarnitine
Propionylcarnitine
Iso-/Butyrylcarnitine
Isovaleryl-/2-Methylbutyrylcarnitine
Hexanoylcarnitine
Octanoylcarnitine
Decanoylcarnitine
Dodecanoylcarnitine
Tetradecanoylcarnitine
Palmitoylcarnitine
Stearoylcarnitine

 

Other hydroxy- and (un)saturated acylcarnitinespecies can also be measured on demand:

3-Hydroxy-butyrylcarnitine Heptanoylcarnitine
3-OH-decanoylcarnitine Hexadecanoylcarnitine
3-OH-dodecanoylcarnitine Hexadecenoylcarnitine
3-OH-hexadecanoylcarnitine Hydroxyisovalerylcarnitine
3-OH-hexadecenoylcarnitine Linoleylcarnitine
3-OH-hexanoylcarnitine Malonylcarnitine
3-OH-linoleylcarnitine Methylmalonylcarnitine
3-OH-oleylcarnitine Octenoylcarnitine
3-OH-stearoylcarnitine Oleylcarnitine
3-OH-tetradecanolycarnitine Suberylcarnitine, propylglutarylcarnitine
3-OH-tetradecenoylcarnitine Succinylcarnitine
Adipylcarnitine, 3-methylglutarylcarnitine Tetradecadienoylcarnitine
Decenoylcarnitine Tetradecenoylcarnitine
Dodecenoylcarnitine Tiglylcarnitine
Glutarylcarnitine  

 

Glycolysis and TCA cycle

TCA cycle-1.jpg

 

Acetyl-CoA Glutaryl-CoA
Citrate Trans-aconitate
Isocitrate Glucose-6-phosphate
Alpha-ketoglutarate Fructose-6-phosphate
Succinyl-CoA Phosphoenolpyruvate
Succinate Pyruvate
Malate Lactate

 

 

 

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Organic acids

Methylmalonic acid

Glutaric acid

2-OH glutaric acid

3-OH glutaric acid

2-methylcitric acid

Tryptophan and kynurenine metabolism & Nicotinate and nicotinamide metabolism

Tryptophan_Nicotinatenicotinamide pathway.png

 

tryptophan nicotinic acid mononucleotide (NaMN, nicotinate ribonucleotide)
kynurenine nicotinic acid adenine Dinucleotide (NaAD, deamino-NAD+)
kynurenic acid NAD+
anthranilic acid nicotinamide mononucleotide (NMN, nicotinamide ribotide)
3-hydroxy-kynurenine nicotinamide riboside (NR, ribosyl-nicotinamide)
xanthurenic acid nicotinamide (NAM, niacin, Vitamin B3)
3-hydroxyanthranilic acid picolinic acid
quinolinic acid glutaryl CoA
nicotinic acid acetyl CoA

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Bile acid metabolism

Bile acids.jpg

Lithocholic acid

Cholic acid

7-Ketolithocholic acid

Glycolithocholic acid

Murocholic acid

Glycoursodeoxycholic acid

Ursodeoxycholic acid

Glycohyodeoxycholic acid

Hyodeoxycholic acid

Glycochenodeoxycholic acid

Chenodeoxycholic acid

Glycodeoxycholic acid *

Deoxycholic acid

Glycocholic acid

Isodeoxycholic acid

Taurolithocholic acid

3-Oxocholic acid

Tauroursodeoxycholic acid

7-Ketodeoxycholic acid

Taurohyodeoxycholic acid

α-Muricholic acid

Taurochenodeoxycholic acid

β-Muricholic acid

Taurodeoxycholic acid

ω-Muricholic acid

Tauro-β-muricholic acid

γ-Muricholic acid

Taurocholic acid

Steroid metabolism

under development

Sphingolipid metabolism

 

Sphingolipids.jpg

SM C6:0 (d18:1/6:0)

DhCer C16:0 (d18:0/16:0)

SM C12:0 (d18:1/12:0)

DhCer C24:1 (d18:0/24:1(15Z))

SM C16:0 (d18:1/16:0)

DhCer C24:0 (d18:0/24:0)

SM C18:1 (d18:1/18:1(9Z))

GlcCer C12:0 (d18:1/12:0)

SM C18:0 (d18:1/18:0)

GlcCer C16:0 (d18:1/16:0)

SM C24:1 (d18:1/24:1(15Z))

GlcCer C18:1 (d18:1/18:1(9Z))

SM C24:0 (d18:1/24:0)

GlcCer C18:0 (d18:1/18:0)

Cer C2:0 (d18:1/2:0)

GlcCer C24:1 (d18:1/24:1(15Z))

Cer C4:0 (d18:1/4:0)

LacCer C12:0 (d18:1/12:0)

Cer C6:0 (d18:1/6:0)

LacCer C16:0 (d18:1/16:0)

Cer C8:0 (d18:1/8:0)

LacCer C24:1 (d18:1/24:1)

Cer C10:0 (d18:1/10:0)

LacCer C24:0 (d18:1/24:0)

Cer C12:0 (d18:1/12:0)

GlcSph C18:1

Cer C14:0 (d18:1/14:0)

Sph (d18:1)

Cer C16:0 (d18:1/16:0)

Sph (d20:1)

Cer C18:1 (d18:1/18:1(9Z))

Spa (d18:0)

Cer C18:0 (d18:1/18:0)

Sph 1P (d18:1)

Cer C20:0 (d18:1/20:0)

Spa 1P (d18:0)

Cer C22:0 (d18:1/22:0)

Cer1P C16:0 (d18:1/16:0)

Cer C24:1 (d18:1/24:1(15Z))

Cer1P C18:1 (d18:1/18:1(9Z))

Cer C24:0 (d18:1/24:0)

Cer1P C24:0 (d18:1/24:0)

Eicosanoid metabolism

under development

Eicosanoids_update.jpg

13-HODE

20-COOH-LTB4

5,6-DiHETE

9-HODE

5,6-DiHETrE

5-KETE

12(13)-EpOME

15-KETE

8(9)-EpETrE

12,13-DiHOME

5-HEPE

9-HOTrE

12-HETE

8-iso-PGE2

8-HDoHE

15-HETE

LTB3

9-KOTrE

5-HETE

LTB4

20-OH-LTB4

9(10)-EpOME

PGE1

13-HOTrE

9,10,13-TriHOME

6-keto-PGF1a

8,15-DiHETE

9,10-DiHOME

PGD2

LTC4

9,12,13-TriHOME

PGD3

14,15-LTC4

9-HETE

PGE2

LTD4

13-KODE

10,17-DiHDoHE

LXA4

9-KODE

11-HDoHE

LXA5

12-HEPE

δ 12-PGJ2

LXB4

15-HEPE

17(R)-Resolvin-D1

18-HEPE

14-HDoHE

11(12)-EpETrE

7,17-hydroxy DPA

17-HDoHE

PGF2a

7-Maresin-1

14,15-DiHETE

11,12-DiHETrE

tetranor-PGDM

EKODE

14,15-DiHETrE

13,14-dihydro-15-keto PGE2

Arachidonic acid

PGE3

tetranor-PGEM

Linoleic Acid

PGJ2

iPF2α-IV

Docosahexaenoic Acid

Resolvin D1

5-iPF2α-VI

Eicosapentaenoic Acid

Resolvin D2

8-iso-PGF2α

TXB2

12(13)-EpODE

8-iso-PGF3α

11B-PGF2a

12(S)-HHTrE

11-dehydro TXB2

15-deoxy-PGJ2

LTE4

TXB3

19,20-DiHDPA

5-HETrE

11-dehydro TXB3

8-HETE

14(15)-EpETE

4-HDoHE

11-HEPE

14(15)-EpETrE

11-HEDE

PGB2

6-trans-LTB4

15-HEDE

PGD1

8,9-DiHETrE

13-HOTrE(γ)

12-KETE

16(17)-EpDPE

15-epi Lipoxin A4

9-HEPE

17(18)-EpETE

TXB1

20-HETE

17,18-DiHETE

FOG9

8-HEPE

19(20)-EpDPE

19-HETE

11-HETE

5(6)-EpETrE

15-OxoEDE

8-HETrE

5,15-DiHETE

14,15-LTE4

15(S)-HETrE

 

 

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Multiple pathway targeted analyses (relative quantification)

Relative quantification of several hundred central carbon metabolites involved in multiple core energy pathways

glycolysis

pentose phosphate pathway

purine and pyrimidine metabolism

TCA cycle

amino acid biosynthesis

OXOPHOS

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Targeted lipidomics (absolute quantification)

Under development

Targeted quantification of  > 1200 lipid species from free fatty acids to complex lipids including glycerolipids (mono-, di- and tri-acylglycerols), glycerophospholipids (phosphocholines, phosphoethanolamines, phosphoserines, phosphoglycerols, phosphoinositols), cholesterol esters and sphingolipids (ceramides, phosphosphingolipids, glycosphingolipids)

Stable isotope-assisted analyses

Isotopic profiling (e.g. 13C tracer analyses) including pathway mapping

Interpretation of labeling patterns (mass isotopomer distributions) of the metabolites of interest involved in central carbon pathways.

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Untargeted analyses

Global central carbon/energy metabolite profiling (HILIC +/- ESI HRMS)

Available only in the context of collaborative research projects

Classes of metabolites

Amino acids and derivatives, carboxylic acids, sugars and derivatives, purines and pyrimidines, nucleosides, nucleotides, redox-electron carriers, etc.

Typical workflow

Data processing

Peak picking, retention time correction, alignment, signal intensity drift correction (within batch), peak annotation

Metabolite screening

AMRT (accurate mass - retention time) in-house database identification (300 - 500 metabolites) + putative matching against available metabolite databases (HMDB, LipidMaps)

Statistical analysis

Univariate statistics (parametric and non parametric tests)

Unsupervised multivariate analysis (PCA, HCA)  Supervised multivariate analysis (OPLS-DA + loadings contribution + model validation)

Complete metabolite identification

MS/MS data acquisition & matching against available libraries (METLIN + in-house updated library)

Pathway analysis

Metabolite set enrichment analysis (MSEA), Pathway topology analysis

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Global lipid profiling (RPLC +/- ESI HRMS)

Available only in the context of collaborative research projects

Classes of metabolites

Phospholipids, sphingolipids, free fatty acids, cholesterol esters, di/triglycerides, acylcarnitines, etc.

Typical workflow

Data processing

Peak picking, retention time correction, alignment, signal intensity drift correction (within batch), peak annotation

Metabolite screening

AMRT (accurate mass - retention time) in-house database identification (300 - 500 metabolites) + putative matching against available metabolite databases (HMDB, LipidMaps)

Statistical analysis

Univariate statistics (parametric and non parametric tests)

Unsupervised multivariate analysis (PCA, HCA)  Supervised multivariate analysis (OPLS-DA + loadings contribution + model validation)

Complete metabolite identification

MS/MS data acquisition & matching against available libraries (METLIN + in-house updated library)

Pathway analysis

Metabolite set enrichment analysis (MSEA), Pathway topology analysis

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Acknowlegment

Targeted method for absolute quantification of bile acids was kindly provided by the Innovation & Development Unit (Clinical Chemistry Service, Department of Laboratories) at CHUV. We gratefully acknowledge Dr. Hugues Henry, Dr. Steve Bruce and Alexandre Béguin for their support with method transfer and setup. We also thank to Dr. Hugues Henry for his precious collaboration during the method development for quantification of amino acid and acylcarnitine panel.

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Switzerland
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