The Metabolomics Core at Baylor College of Medicine is an analytical facility specializing in liquid chromatography hyphenated with mass spectrometry techniques. Its main role is to support investigators in their research in the study of metabolism, as well as an understanding of the mechanisms of particular cancer states, which will ideally lead to earlier detection and better treatments. The core has established methods for targeted measurement of over 500 metabolites, metabolic flux, and drug metabolism and pharmacokinetics (DMPK) in diverse biological specimens using established protocols, methods and mass spectrometry as the primary platform.

Procedurally, the core personnel perform extraction of metabolites from biological samples using a combination of aqueous and organic solvents, carry out the mass spectrometry analysis, and pre-process the mass spectral data. The entire process starting from sample preparation to mass spectrometry is monitored using spiked isotopic standards that have been characterized for their chromatographic behavior and fragmentation profile. Once the mass spectral data is obtained, various data analytics steps namely scaling, imputation and normalization are performed using Mass Hunter software and the resulting output is passed on to an in-house biostatistics pipeline, that then computes the data to determine metabolite levels, and define differential compounds. This Tier 1 level of data analysis is provided as part of routine Core service. Upon request, additional advanced Tier 2 level data analysis can be provided separately by our bioinformatics group. Tier 2 analysis can include pathway mapping using multiple enrichment methods that include Oncomine Concept Map (OCM), Ingenuity (IPA), Gene Set Analysis (GSA), and Network-based Gene Set Enrichment Analysis (NETGSEA). Tier 2 data analysis can also support the integration of transcriptomic and proteomic data (if available with the investigator) with the metabolomics data.

Technology and Infrastructure

The main platforms are Agilent 6490 triple quadrupole (QQQ) mass spectrometers connected to an Agilent UPLC. The QQQ has a wide dynamic range of mass detection from 5-1,400 amu, six orders of linearity and a high mass resolution of ~0.4 amu, for detection of metabolites in a targeted approach. In addition, we have a 2000 compounds MS2 library from Agilent.

Targeted Metabolomics

Targeted Metabolomics serves all researchers at Baylor College of Medicine by providing services to perform quantitative measurements of known compounds through the use of high-pressure liquid chromatography and mass spectrometry. The established the below-listed methods by standard protocols and encourages the development of new protocols to quantity additional compounds.

Classes of Metabolites Measured

Methods


Tissues (10 samples cost)

Cells (10 samples cost)

Serum /plasma/Urine (10 samples cost)

Assay 1.

Amino sugar - Positive ionization

$450

$338

$300

Assay 2.

Amino sugar - Negative ionization

$450

$338

$300

Assay 3.

Amino acids and related metabolites - Positive ionization

$450

$338

$300

Assay 4.

Amino acids and related metabolites - Negative ionization

$450

$338

$300

Assay 5.

Prostaglandins

$563

$431

$375

Assay 6.

Carnitines (Short chain)

$563

$431

$375

Assay 7.

Polyamines

$563

$431

$375

Assay 8.

TCA metabolites

$563

$431

$375

Assay 9.

CoA's and Carnitines (Long chain)

$563

$431

$375

Assay 10.

Sugars

$563

$431

$375

Assay 11.

Nucleotides / Nucleic acid

$563

$431

$375

Assay 12.

Vitamins and Steroids

$563

$431

$375

Assay 13.

Bile acids

$563

$431

$375

Assay 14.

Short-Chain Fatty Acids

$563

$431

$375

Assay 15.

Methylated Metabolites

$563

$431

$375

Assay 16.

Polycyclic aromatic hydrocarbons

$563

$431

$375

Metabolites Require method development


$60/metabolite

$60/metabolite

$60/metabolite

Note: 1) Given Price for relative measurements. 2) Additional cost for absolute concentrations of each metabolite and need to discuss with core director. The cost will vary for the new metabolites which are not included in these assays.

Metabolic Flux

To test mechanisms that are responsible for altered regulation of steady-state levels of metabolites, in the cell, measurements of metabolic flux through pathways is required. By providing 13C or 15N isotope labeled metabolic substrates (such as isotopic labeled glucose, glutamine, or lactate) to living cells, isotopomer patterns of key metabolites can be precisely measured using mass spectrometry. These analyses can provide valuable information on both pathway activities and metabolite pool sizes.  Since all metabolites are either reactants or products in metabolic pathways, changes in their levels due to either altered production or altered disposal are determined by the kinetic rates of key steps within those pathways. Services available currently use cell lines only and are confined to the targeted analysis of pathways as indicated below: (and view the Metabolic Flux Service page).

  • Glucose metabolic flux
  • Citric acid cycle (TCA cycle) metabolic flux
  • Glutamine Flux
  • Lipid or Fatty acid Metabolism

Lipidomics

Untargeted LC-MS Based Shotgun Lipidomics

Lipidomics approaches can provide valuable new insights into the role of lipid molecular species in human health and disease and may identify potential lipid biomarkers that can be developed for diagnostic/prognostic and therapeutic use. Our strategy is to use a ABSCIEX 5600 triple TOF MS that combines high-sensitivity detection, high resolution with the fast acquisition speeds, and stable mass accuracy over days of acquisition accompanied by RP-UPLC methodology. Identification of lipids is accomplished by data-dependent product ion (MS/MS) information of human plasma, tissues, and urine lipid species in both positive and negative ionization modes. During the electrospray ionization, molecular ion adducts such as [M+H]+, [M+Na]+ and [M+NH4]+ or [M−H]−, and [M+CH3COO]− are formed in both positive and negative modes. Data-dependent MS/MS acquisition or MS/MS ALL acquisition provides information on the nature of the head group and/or neutral loss of the head group from the molecular ion adducts. The information on fatty acids composition of the lipids is obtained in the negative mode.  (View the Lipidomics service page.)

When you're ready to proceed, please follow the steps to submit a project service request through iLab.