Dr. Milburn discussed some of the advantages of studying metabolites as opposed to proteins or gene expression. Biochemical molecules are the end result of many biological processes, and they can reflect the impact of a number of factors, such as the environment, a patient’s overall health, and any drugs a patient might be taking. While the technology used to analyze the human metabolome is complex, the metabolome is smaller than the genome or the proteome. According to the most recent estimates, there are only about 2,400 metabolites in the human body—significantly fewer than the approximately 25,000 genes, 100,000 transcripts, and millions of proteins with which other fields must work.

In a sense, metabolomic analysis can be thought of as an expansion of the traditional diagnostic tests performed on blood or urine and used to measure the levels of, for example, blood urea nitrogen, creatinine, and glucose. While these molecules represent a small portion of the total biochemistry of the body, the aim of metabolomics is to look at all, or at least a large proportion, of the body’s small molecules.

The Metabolon Process

At Metabolon, the goal is to be able to identify and quantitatively measure all of the small molecules in any sample type—urine, blood, tissue, or cell extract. The process used is illustrated in Figure 5-1. Sample preparation begins with four different fractionation steps to extract all polar and nonpolar molecules with a mass of 50–1,500 daltons. Once these small molecules have been separated out through these four extraction steps, they are pooled back together, and that sample is then split for analysis by two different platforms—a liquid chromatography–mass spectrometry system (LC-MS) and a gas chromatography–mass spectrometry system (GC-MS). Company scientists use both of these platforms because small molecules can be very polar as well as very nonpolar; the two chromatography methods work well together for profiling of most of the small molecules in the samples.

Metabolon has developed proprietary software that makes it possible to identify automatically all the ions that are scanned by the spectrometers. Using automated processing techniques based on the biological variation of the compounds within samples, the researchers are able to reconstruct the original molecules to which the ions belonged before going through the system. With the help of a standard chemical library,


This section is based on the presentation of Michael Milburn, Chief Scientific Officer, Matabolon.

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