Targeted Metabolomics

This service is provided by the Biomarkers Core Laboratory.


Targeted metabolomics is the hypothesis-driven, absolute quantitative assessment of a subset of metabolites often linked to a metabolic pathway (glycolysis, TCA cycle).

Biomarkers Core Laboratory (BCL) offers several Liquid and Gas Chromatography-Mass Spectrometry (LC-MS/MS, GC-MS/MS) based targeted metabolomics assays to support preclinical, clinical and translational research. Core services also include the method development and validation of novel mass spectrometry based targeted quantitative assays for the metabolites of your interest.

Our targeted metabolomics assays involve a reverse phase or HILIC based chromatographic separation followed by either selective or multiple reaction monitoring (SRM or MRM) in positive or negative electrospray ionization mode, depending on the nature of the analyte(s). The quantitative approach is based on the use of stable isotope labeled internal standards (13C, 2H) and external reference standards. Core customizes the sample preparation protocols (protein precipitation, Liquid-Liquid extraction and Solid Phase extraction) based on the physicochemical properties of the compound, their abundance, and the sample type among other factors.

Starting in March 2020, the BCL is also providing support for COVID-19 research. 

Metabolomics Assays

BCL offers several targeted LC-MS /MS based assays for individual biomarkers, as well as panels targeting specific classes of metabolites. These assays are validated against a wide range of sample types including body fluids (plasma, serum, saliva, urine), cells, and various tissue types from human subjects and research animals.

The major metabolomics panels and the analytes include:

Biocrates MxP® Quant 500 metabolites Kit: BCL offers a comprehensive targeted metabolite quantitation using the MxP® Quant 500 kit (BIOCRATES Life Sciences AG, Innsbruck, Austria) with a coverage of up to 630 metabolites from 26 analyte classes. The Q500 kit is validated for use with both human and animal plasma, serum, tissue, feces, and cells. Metabolite coverage includes aminoacids and aminoacids related (#50), bile acids (#14), acylcarnitines (#40), fatty acids (#12), phosphatidylcholines (76), and triglycerides (242). The complete list can be found here.

Biocrates AbsoluteIDQ p180 metabolites kit: BCL can perform simultaneous targeted quantitation of upto 188 endogenous metabolites using the Absolute IDQ p180 kit (BIOCRATES Life Sciences AG, Innsbruck, Austria). The kit has been validated for plasma, tissue, and cells and require only 10ul of sample, especially suited when sample volume is a limiting factor. It includes aminoacids (#21), biogenic amines (#21), hexose (#1), acylcarnitines (#40) and sphingolipids (#15) and glycerophospholipids (#90 species).

Bile acids: BCL offers a well validated metabolomics panel for the targeted quantitation of bile acids from human and murine plasma, serum, tissues, feces and bronchial washings. Analytes include CA, DCA, UDCA, HDCA, LCA, TLCA, TCDCA, GCA, TDCA, GDCA, TCA, GCDCA, GUDCA, TUDCA, (α+Ɯ)-MCA, β-MCA, and T(α+β)-MCA.

Acylcarnitines: Carnitine (C0), Acetylcarnitine (C2), Propionylcarnitine (C3), Butyrylcarnitine (C4), Isovalerylcarnitine (C5), Octanoylcarnitine (C8),  Myristoylcarnitine (C14), and Palmitoylcarnitine (C16)

Aminoacids:  Histidine, Arginine, Asparagine, Glutamine, Serine, Aspartic acid, Citrulline, Glutamic acid, Threonine, Alanine, Proline, Cystine, Lysine Tyrosine, Leucine, Isoleucine, Valine, Methionine, and Glycine

Biogenic amines: Dopamine, Epinephrine, Norepinephrine, Tryptophan, Kynurenine, Serotonin, Putrescin, Spermine, and Spermidine

Sphingolipids: Sphingosine, Sphinganine, Sphingosine -1-Phosphate, Sphinganine-1-Phosphate, C14 Ceramide, C16 Ceramide, C18:1 Ceramide, C20 Ceramide, C24 Ceramide, and C24:1 Ceramide

Free Fatty acids: Lauric acid (C12:0), Myristic acid (C14:0), Palmitic acid (C16:0), Palmitoleic acid (C16:1), Stearic acid (C18:0), Oleic acid (C18:1), Linoleic acid (C18:2), alpha Linolenic acid (C18:3), Arachidic acid (C20:0), Arachidonic acid (C20:4), Eicosapentaenoic acid (C20:5), Adrenic acid (C22:4), Docosapentaenoic acid (C22:5), and Docosahexaenoic acid (C22:6).

Organic acids: Citric acid, Fumaric acid, Succinic acid, Malic acid, Oxaloacetic acid, α-Ketoglutaric acid, Aspartic acid, 2-Hydroxyglutaric acid, and Glutamic acid.

Steroids: Estradiol, Ethinyl estradiol, Progesterone, Testosterone, Estrone

Vitamin D metabolites: 25-hydroxyvitamin D2, 25-hydroxyvitamin D3, 1,25-dihydroxyvitamin-D3, 1,25-dihydroxyvitamin-D2, and 24,25-dihydroxyvitamin-D3

Note: In few instances, metabolites included in the same class are run as different assays due to their dynamic range or chromatographic properties.

Protein Turnover Kinetics:

BCL offers GCMS and LCMS based platforms to support metabolism studies using stable isotopes to examine protein turnovers. Our current enrichment assays include apolipoproteins; apo(a), ApoB100, ApoC2, ApoC3, and PCSK9. Please contact us for more information.


BCL houses four LCMS and one GCMS Triple Quadrupole (QQQ) mass spectrometers integrated with either UPLC, nanoLC or GC systems for performing targeted metabolomics assays.

Waters Xevo TQ-S

Waters Xevo TQ-S

Xevo TQ-S MS from Waters Corporation features a StepWave ion guide that delivers the highest levels of sensitivity and robustness. It also has an innovative ScanWave™ collision cell technology to provide enhanced spectral LC-MS/MS data acquisition capabilities. At BCL, the TQ-S MS is integrated with Waters® Acquity UHPLC system for the sensitive detection of steroids, contraceptive drugs, and neurotransmitters among others. Integration of TQ-S with Waters® nanoacquity UPLC through the ionKey source allow us to employ the 150uM I. D. plug and play iKey separation device enabling highly efficient, sensitive microflow separations for the low abundant protein turnover applications.


Waters Xevo TQ-MS

Waters Xevo TQ-MS

Xevo-TQ MS is a triple quadruple (QQQ) mass spectrometer designed for routine quantitative UPLC-MS/MS applications involving low concentrations of target compounds in highly complex and diverse samples. It features the ScanWave® collision cell and T-Wave™ technology supporting both quantitative and qualitative studies. Integration of TQ-MS with Waters® Acquity UPLC allow us the sensitive quantitation of a wide range of small molecule biomarkers and drugs.


ABSciex API 4000 LCMS

ABSciex API 4000 LCMS

The API4000 MS a robust, high throughput, and sensitive instrument for the accurate and precise quantitation of small molecules in complex clinical samples. It is characterized by enhanced ionization efficiency, high flow-rate performance, wide scan range, self-cleaning probe design, and reliable interface combined to reduce maintenance time, accelerated productivity and high throughput. Paired with Eksigent UltraLC 100, it enables the confident quantitative assessment of small molecule metabolites and drugs in body fluids and a variety of tissues.


Agilent 7890A/7000B GCMS

Agilent 7890A/7000B GCMS

The Agilent 7890A/7000B GCMS system is a gas chromatograph coupled to a mass selective detector allowing both Electron Impact Ionization (EI) as well as Chemical Ionization (CI). It features MRM speed at 500 transitions per second, with a minimum dwell time of 1msec and zero cross-talk providing reliable quantitation for targeted metabolomics assays. 


The BCL is open Monday – Friday, 9am to 5pm. Samples may be dropped off during these hours and dry ice must be used during transportation.

Eligibility and Requirements

Targeted metabolomics services are available to all researchers at Columbia University and at other academic institutions.   

Investigators that are not affiliated with Columbia University will need to complete a service agreement that must be signed by the legal or purchasing departments of both parties. This process takes approximately four weeks to finalize. The requestor’s legal or purchasing department’s service agreement template is typically used, but one can be provided by Columbia if necessary. For more information on service agreements and pricing for non-CU initiated studies, please email the BCL director, Dr. Renu Nandakumar.

The BCL is not Clinical Laboratory Improvement Amendments (CLIA)-certified. The data generated from BCL is to be used for research purposes only and not for clinical and diagnostic applications.

Submitting Requests

A new protocol submission request must be initiated in iLab for every new project. Samples will not be accepted without an active service request. Additional request details forms must be submitted if more assays or samples need to be added to an existing protocol. Please contact us for the instructions on how to register and submit a service request through iLab.

Sample Submission

Please review the BCL’s User Policy and General Sample Submission Guidelines prior to submitting the samples and complete the downloadable sample list template to be delivered along with your samples.

When to Request This Service

We strongly encourage investigators to contact BCL director, Dr. Renu Nandakumar, prior to submitting a new service request. This will facilitate a discussion on the project, scope, feasibility, appropriate analytical strategy and other sample requirements. Please set up a consultation to initiate new metabolomics projects involving LCMS method development.


A complete list of the mass spectrometry-based assays and associated cost is available on our downloadable price list. If you do not find the assay that you are interested in, please contact us and we will work with you to explore your options.

Cite it, Submit it, Share it!

If your research has benefited from one or more Irving Institute resources, please remember to:

  • Cite our CTSA grant, UL1 TR001873, in any relevant publications, abstracts, chapters, and/or posters.
  • Submit your publications to PubMed Central (PMC) for compliance with the NIH Public Access Policy.
  • Share your research updates with us by sending an email to:


Biomarkers Core Laboratory
622 West 168th Street, 10th Floor, Room 105
Presbyterian Hospital Building, PH10-105
New York, NY 10032
United States