“There are a lot of small molecules that we do not even know about yet,” says Arthur Castle, programme director for the Roadmap Metabolomics Technology development programme at the US National Institutes of Health in Bethesda, Maryland. Metabolomics has a good handle on analysing human primary metabolites, but when it comes to lipids, secondary metabolites, xenobiotics and the products of gut microflora, we are just scratching the surface, says Castle.

The problem is part technological, part informatics. Steven Fischer at Agilent Technologies in Santa Clara, California, points out that some compounds are not stable and undergo chemical transformation during separation. Researchers will probably still see these transformed molecules by mass spectrometry (MS), but they may be misidentified, highlighting the need for follow-up experiments. And this is where metabolomics has an advantage over the other 'omics'. “There is so much knowledge of biochemistry that when we find a potential biomarker or a new drug mechanism we already know a lot about it,” says Michael Milburn, chief scientific officer at Metabolon in Durham, North Carolina.

NIMS: nanostructured surface releases material. Credit: REF. 4

Trent Northen, now at the Lawrence Berkeley Laboratory in Berkeley, California, and Oscar Yanes, working in Gary Siuzdak's lab at the Scripps Research Institute in La Jolla, California, may have developed a new way to get at some of these 'unknown' molecules with an ionization technique called nanostructure-initiator mass spectrometry (NIMS)4. The idea is to transfer a biomolecule into the gas phase from a nanostructured surface simply by making that surface disappear. “We came up with the idea of putting a wax underneath, so when the nanostructured surface was irradiated it would melt and vaporize, allowing the molecule to go into the gas phase,” says Northen. They finally came up with a perfluorinate surface for the trapped initiator phase.

Siuzdak's group found that NIMS worked not only for proteins, but also for small molecules such as metabolites. “Perfluorinates do not ionize well, so it allows us to see things in the lower mass region where metabolites like to hang out,” says Siuzdak.

Using perfluorinated materials may have another advantage for metabolomics. “As these are highly hydrophobic surfaces, we can apply very dirty complex samples, such as blood, for direct analysis,” says Yanes. If you put a drop of urine or blood on the NIMS chip the metabolites will attach, but all the salts and other chemicals that normally interfere with MS stay in solution. Yanes is now exploiting this property to follow drug metabolism by looking at uptake in blood, clearance in urine and tissue localization.

For Siuzdak, exploring the 'unknown' metabolite world is an exciting prospect. “We are getting involved in an area where we don't know what the molecules' structures are or what they do, so it is really just a fantastic area for discovery.”

N.B.