Christine Brideau, biochemistry and molecular biology research fellow at the Canadian subsidiary of Merck & Co., compared different cutting edge MS techniques and outlined how the company has used them to identify lipid enzyme inhibitors. The results were recently presented at the Drug Discovery and Development of Innovative Therapeutics (DDT) conference, Boston, US.

She explained that if a drug target is not amenable to ultra high-throughput screening (UHTS) techniques, it is unlikely to be tested against a firm's entire compound library. This clearly reduces the chances of finding a compound that binds strongly to the target and might be useful as a drug.

Brideau went on to say that another disadvantage to traditional UHTS is that the assay often has to be designed based on robotic capabilities. Other challenges include if there are no known ligands for new targets; the cost of substrate synthesis and reagent acquisition times.

As Brideau explained, all this has meant that: "At Merck-Frosst, several targets have proved very challenging to design assays for."

These included 5-HETE, desaturases, methyl-transferases, COX-2 and PGE Synthase - these last two due to the instability of PGH2. One possible answer is label-free screening using MS, as this enables scientists to represent a more natural biological system. It also saves time and money because there's no radioactive waste, according to Brideau.

However, traditional MS takes at least two minutes per sample and so can't be described as high-throughput. Several companies are working to improve this speed, for example, at BioTrove, where Brideau said scientists have achieved screening speeds of one sample per six seconds using its RapidFire system. This equates to 15 384-well plates per day or 50 minutes per plate.

In fact, Merck-Frosst has been collaborating with BioTrove to design a phosphatidylethanolamine methyltransferase (PEMT) assay, using a 384 well plate; a good signal to background ration indicated a high quality assay, according to Brideau.

Merck-Frosst didn't test only this technology; they also collaborated with Shimadzu, using its Prominence HPLC system. Merck-Frosst believes this tool has the fastest sample injection cycle and the ability to stack up to 12 plates leads to a testing time of 27 seconds per sample.

Although this still leaves BioTrove's RapidFire as the higher throughput machine, it is lower precision on injection. Although there is no LC separation, this means sample preparation is faster.

"No single high-throughput MS technology works for all samples, they are complementary," said Brideau. "If the scientist doesn't need separation, they have more choice."

Phytronix and MDS Sciex have also developed high speed MS products. According to Merck-Frosst's research, for a 96-well plate, Shimadzu is the slowest - at 42.5 minutes, followed by Phytronix (25 minutes) and BioTrove (10 minutes). The quickest is MDS Sciex's MALDI (matrix-assisted laser desorption-ionisation) MS machine, with a run-time of around five minutes. Although Brideau maintained that the reproducibility remains to be evaluated and that the technique requires some sample preparation is required.

She also believes that none of these systems is "high throughput enough" as researchers can only do 96-well plates.

"There is a lack of fully integrated MS systems for high throughput screening labs. Throughput can be increased via multiple parallel systems to match UHTS."

To achieve this, Brideau believes it is crucial to have expert assay development, which might require outsourcing the work, and also to work with the vendors to develop their technology.