Targeted analysis Is performed to analyze or quantify specific metabolites. The instruments used for targeted analysis are NMR, GC/MS and LC-MS/MS. Targeted analysis depends on the following:

1. The ability to obtain authentic or synthetic standards
2. The ability to detect the standard (using any of the listed instruments)
3. The ability to efficiently extract the endogenous compound(s) from the sample(s) and derivatize if necessary (GC/MS).
4. The ability to have good chromatography (either GC or LC) of the endogenous compounds to cleanly separate them from other confounding metabolites.

For more information on how we use our instrumentation for targeted analysis, please have a look at this link.

We have attempted to group targeted metabolites into logical families. The families tend to be grouped either by metabolic pathway or chemical behavior or class. Note that there is overlap between groupings. When more than one analysis is requested, we do our best to try to analyze as much as possible from the given sample. A 30% discount is applied to second and/or subsequent analysis sets when it is possible to acquire the data using similar chromatography, sample preparation and the same instrumentation.

If you cannot find the metabolites you are interested in targeting, please make an appointment to talk with us. Our group has the expertise to create new methodologies specific to your needs. Custom analysis charges will apply (staff & instrument time) unless otherwise directed by the MCF oversight committee.

The MCF offers both free and total amino acid analysis either by NMR, GC/MS or LC/MS depending on other desired analyses. The current library of amino acid and amino acid derivatives are listed

alanine, beta-alanine glycine phenylalanine
allo-isoleucine histidine phospho-serine
arginine homocysteine proline
asparagine homocystine pyroglutamate
aspartic acid hydroxyproline sarcosine
betaine hypotaurine serine
citrulline isoleucine taurine
cysteine leucine threonine
cystine lysine tryptophan
glutamic acid methionine tyrosine
glutamine ornithine valine
gamma-aminobutyric acid


The citric acid cycle intermediates may be measured by LC/QQQ or GC/MS.

Note that oxaloacetate, pyruvate and a-ketoglutaric are not stable intermediates. For GC/MS analysis these intermediates are reduced using NaBD4 to their more stable alpha-hydroxy acids.

The intermediates are quantified by stable isotope dilution (ref:

The following metabolites are quantified:

Lactic acid Alpha-ketoglutaric acid
Pyruvic acid Succinic acid
Citric acid Fumaric acid
Isocitric acid Oxaloacetic acid
Oxaloacetic acid* Malic acid
2-hydroxyglutaric acid  

*Oxalosuccinic acid can be quantified but we have not detected it reliably, to date, in eukaryotic cells or tissue extracts.

Fatty acids generally vary in length from 4 to 28 carbons with various levels of unsaturation.  Free fatty acids can be metabolized as a fuel (free fatty acids) or used as building blocks for cell walls, tri-glycerides and other lipids.  Saponification allows for full fatty acid analysis compared to the generally lower level of free fatty acids. 

The MCF provides GC/MS based untargeted analysis for fatty acids.  Our fatty acid library is listed below.  Other fatty acids of special interest can be added to our library assuming an authentic standard can be obtained. 

Currently we provide ratios of fatty acid to an internal standard (D27-myristic).  Absolute quantitation can be done by special request.

Current list of fatty acids in our library (more can be added!):

Montanic C28:0 Eicosapentaenoic C20:5 {{5,8,11,14,17}} Palmitic C16:0
Cerotic C26:0 Eicosapentaenoic C20:5 {{5,8,11,14,17}} Stearic C18:0 Palmitoleic C16:1 {{9}}
Lignoceric C24:0 Oleic C18:1 {{9}} Palmitelaidic C16:1 {{t9}}
Nervonic C24:1 {{15}} Petroselinic C18:1 {{6}} C15:0
Behenic C22:0 Vaccenic C18:1 {{11}} Myristic C14:0
Erucic C22:1 {{13}} Linoleic C18:2 {{9,12}} Myristoleic C14:1 {{9}}
Arachidic C20:0 α-Linolenic C18:3 {{9,12,15}} C13
Eicosenoic C20:1 {{11}} γ-Linolenic C18:3 {{6,9,12}} Lauric C12:0
Eicosatrienoic C20:3 {{8,11,14}} Margaric C17:0 Capric C10:0
Arachidonic C20:4 {{5,8,11,14}}   Caprylic C8:0
β-Hydroxy Acids
Decanoic C10:0 3-OH Undecanoic C11:0 3-OH Lauric C12:0 3-OH
Myristic C14:0 3-OH C15:0 3-OH Palmitic C16:0 3-OH


Glycolytic intermediates are measured by LC/QQQ and quantified by external calibration curves. Due to structural and molecular weight similarity it is not possible to resolve some intermediates.

Note also that glycolytic intermediates are normally found at very low concentrations, and therefore may be difficult to measure.

The intermediates in our protocol are as follows:

Glucose Glyderaldahyde 3-phosphate
Glucose 6-phosphate / Fructose 6-phosphate Dihydroxyacetone phosphate
Fructose 1,6 bis-phosphate Phosphoenolpyruvate
2-Phosphoglycerate Pyruvate
3-Phosphoglycerate Lactate


The nucleotide analysis includes many mono, di and triphosphates, such as ATP, ADP and AMP for energy charge analysis.
This analysis also includes creatine and phosphocreatine since the ratio of these metabolites also contributes to the energy charge of the cell. Nucleotides are measured by LC/QQQ and quantified based on external standard calibration curves run at the same time as the samples of interest.

Our current library of nucleotides is listed below.
We can add additional nucleotides upon request assuming authentic standards are available.

Adenosine monophosphate 
Inosine 5’ monophosphate
Flavin adenine dinucleotide
Adenosine diphosphate
Inosine 5’ diphosphate
beta-Nicotinamide adenine dinucleotide
(NAD+ )
Adenosine triphosphate
Inosine 5’ triphosphate
beta-Nicotinamide adenine dinucleotide reduced
Adeosine 3,5, cyclic monophosphate
Cytidine 5’ monophosphate
beta-Nicotinamide adenine dinucleotide phosphate
(NADP+ )
Guanosine monophosphate
Cytidine 5’ diphosphate
beta-Nicotinamide adenine dinucleotide phosphate reduced
Guanosine diphosphate
Cytidine 5’ triphosphate
Uridine 5’-diphosphoglucose
Guanosine triphosphate
Thymidine 5’ monophosphate
Uridine 5’- diphosphogalactose
(UDP-galactose )
Uridine 5’ monophosphate
Thymidine 5’ diphosphate
Uridine 5’- diphosphoglucuronic acid
(UDP-glucuronic acid )
Uridine 5’ diphosphate
Thymidine 5’ triphosphate
Uridine 5’ diphospho–N-acetylglucosamine
(UDP-N-acetyl glucosamine)
Uridine 5’ triphosphate


The nucleoside analysis includes the nitrogenous bases, ribonucleosides, and deoxyribonucleosides. Nucleosides are measured by LC/QQQ and quantified based on external standard calibration curves run at the same time as the samples of interest.

Our current library of nucleosides is listed below. We can add additional nucleotises upon request assuming authentic standards are available.

Adenine Adenosine 2'-Deoxyadenosine
Guanine Guanosine 2'-Deoxyguanosine
Cytosine Cytidine 2'-Deoxycytidine
Thymine 5-Methyluridine 2'-Deoxythymidine
Uracil Uridine 2'-Deoxyuridine


Please note that some metabolites listed here are redundant to the Amino Acids analysis. We attempt to capture reduced and oxidized forms of important metabolites involved in reducing oxidative stress.

These partially cover folate metabolism and the methionine cycle.
Taurine and hypotaurine can be easily added upon request

Reduced Glutathione Cystathionine Folate
Oxidized Glutathione Homocysteine Dehydrofolate
Ascorbic Acid Methionine Tetrahydrofolate
Dehydroascorbic acid S-adenosylmethionine (SAM)  
Cystine S-adenosylhomocysteine (SAH)  
Cysteine gamma-glutamylcysteine  


* Image from


The pentose phosphate pathway intermediates are quantified by LC/QQQ using external calibration curves.  The following metabolites may be measured: 

Glucose Ribose
Glucose-6 phosphate Ribulose
5-Phospho-D-Ribose 1 diphosphate Glucosaminic Acid
6-Phosphogluconic acid Ribose 5-phosphate
Gluconate Ribulose 5-phosphate
Gluconolactone 2-Deoxy-ribose 5-phosphate
Sedoheptulose 7-phosphate 2-Deoxyribose


The short chains CoAs are analyzed by LC-MS/MS and quantified against external calibration curves.  The following CoAs are currently analyzed (others may be added upon request assuming the availability of authentic standards):

Aceto-Acetyl CoA Malonyl CoA
Acetyl CoA Propionyl CoA
Butyryl CoA Succinyl CoA



Currently under development for analysis by GC/MS - The steroids we currently are working with are as follows:

17-OH-progesterone Estrone
Aldosterone Hydrocortisone
Corticosterone Pregnanedione
Cortisone Pregnenolone
Equilin Progesterone
Estradiol Testosterone