Metabolomics Core

Overview of Services

Metabolic Measurements Using Targeted Mass Spectrometry (Metabolomics)

The mass spectrometry-based metabolomics portion of the core will allow targeted measurement of candidate metabolites likely to be key to detection or disease progression. This will be directed by Dr. Nagireddy Putluri using protocols and similar MS instrumentation using a validated pipeline.

The laboratory currently measures over 300 metabolites using the targeted multiple reaction monitoring approach (MRM). MRM provides the lowest limits of detection with the highest confidence in metabolite identification. The laboratory has the capability for additional method development and has developed robust methods for handling cell line, flash frozen-tissue and plasma, specimens that will be routinely encountered in a core setting. The minimum amount of sample required for each of these matrices, to measure at least 10 metabolites is given below:

• Cell lines: 2 to 5 million
• Tissue: 10 to 25 milligrams
• Plasma: 100 to 500 ul

Procedurally, the investigator will be asked to provide the core with the biological specimen. The core personnel will perform extraction of metabolites from biological samples using a combination of aqueous and organic solvents in succession and carry out the mass spectral analysis and associated data pre‐processing. At the end of this pre-processing step, the investigator will be provided an excel file containing raw data for the metabolites measured in the biospecimen. Upon request, the core will also provide statistical help to analyze this data by performing, the various pre‐processing steps namely scaling, imputation and normalization determine class-specific metabolite levels. The latter will carried out by a biostatistician associated with the core on a fee-for service basis. Also whenever possible, upon request the core will also develop new methods to quantify additional metabolites. Because of the chemical diversity of metabolites, new method conditions will need to be determined on a case‐by‐case basis and would involve a determination of ionization conditions, single reaction monitoring (SRM) fragmentation conditions and mass transitions, and chromatographic behavior. For absolute quantification of specific metabolites, an additional fee for procurement of isotopic-labeled standards will be included.
The entire mass spectrometry-based metabolite-assessment will be performed on an Agilent 6490 triple quadrupole (QQQ) mass spectrometer based on instrument availability and the time line will be determined by the core director.

References:

1. Sreekumar A, et.al " Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression" Nature. 2009 Feb 12; 457(7231):910-4.
2. Putluri N, et. al " Metabolomic profiling reveals potential markers and bioprocesses altered in bladder cancer progression" Cancer Res. 2011 Dec 15; 71(24):7376-86. Epub 2011 Oct 11.

Getting Started

• BCM Users:  Click the link in the upper right corner to login or register for an iLab account using valid BCM credentials.

• Non-BCM Users:  Click the appropriate link in the upper right corner to login with your approved iLab credentials or to sign up for an iLab account.

• Visit the Customer Help Manual for further guidance using iLab's Core Facility Services.

Location and Hours of Operation

Links and Resources

• Visit our BCM core website for additional information.

Publication Acknowledgements

Scientific publications containing data obtained using the services offered by the core should include the following statement in the acknowledgment section: This project was supported by the Metabolomics Core at BCM.

Contacts