MDS Proteomics Opens Flagship Functional Proteomics Facility Outside Toronto

At a ceremony earlier this month featuring guided tours and a discussion moderated by Eric Lander, MDS Proteomics officially unveiled its new global headquarters and functional proteomics center in Toronto.

With 52,000 square feet of working space for 140 of the company’s global staff of 225, the Toronto proteomics factory is by far the largest of MDS’ four facilities in North America and Europe, but still has room to grow. “Everything we have built has been constructed to be scaleable,” said Mike Moran, MDS Proteomics’ chief scientific officer and senior vice president for discovery research.

The space holds more than 30 MDS Sciex and Thermo Finnigan mass spectrometers designed to collect high-throughput data on protein-protein interactions, protein-drug interactions, protein modifications, and protein locations within cells. The range of instruments includes triple-quadrupole, ion trap, Fourier transform mass spectrometers, and “a range of off-the-shelf commercial type instruments all the way through to prototype instruments,” said Moran.

Unlike Celera and GeneProt, two of MDS’ putative rivals in discovery proteomics, the new MDS facility does not currently contain MALDI-TOF/TOF mass spectrometers.

Gel or No Gel?

 The Toronto facility is devoid of 2D gel electrophoresis equipment, Moran said, but heavily populated with 1D gel electrophoresis and Agilent high-performance liquid chromatography systems for separating proteins. “The [background] noise that is introduced by [2D gels] just makes it incompatible with detecting low amounts of proteins. Our mass spectrometry capability is much more sensitive,” said Moran.

In fact, MDS is trying to move away from gel electrophoresis altogether, despite having its own robot for processing 1D gels. “We’re probably generating a substantial amount of data now not using any gels,” said Moran. “We’re very much looking towards a gel-free platform.”

Apart from protein analysis tools, the facility also has standard molecular and cell biology equipment, including automated human cell culturing.

Computing power also occupies substantial space in the Toronto facility. Two of the company’s three IBM eServer Linux clusters with 400 nodes are located in Toronto; a third with 200 nodes is located in the company’s other large proteomics analysis center in Odense, Denmark.

Although the Odense facility is also dedicated to large-scale functional proteomics, that location offers only 35,000 square feet for the approximately 75 scientists who work there. The Danish facility has particular responsibilities for developing new mass spectrometry techniques and analyzing cellular compartments and organelles, Moran said.

The company’s smallest facility, in Charlottesville, Va., is currently located on the University of Virginia campus, where MDS scientific advisor Don Hunt operates an academic laboratory. That facility, which also specializes in mass spectrometry development, will move to slightly larger premises within the next few months.

Plans for Moving Downstream

 MDS also operates a small drug discovery laboratory in Boston, and Moran said that facility would expand as the company moves downstream into therapeutics. “Our mission is really to be a drug discovery company,” he said. The company’s first therapeutics, he hopes, will be human monoclonal antibodies developed over the next five years in collaboration with Abgenix, MDS’ first pharma partner, followed eventually by small- molecule drugs.

The newly-opened Toronto facility originated as a MDS pilot facility at Toronto’s Mount Sinai Hospital, where Tony Pawson, one of the company’s founders, has a laboratory. It was Pawson’s academic research into protein function that led MDS Sciex to initially supply his lab with prototype spectrometers, Moran said, and that “led to the rapid development of what has become the Toronto compartment of MDS Proteomics.” As the staff grew to 100, MDS relocated first to an adjacent building before moving into the company’s new location outside Toronto in September.

MDS has already completed research “demonstrating our functional proteomics approach on model organisms,” Moran said, which he hopes will be published soon. Ultimately, Moran prefers to have the company’s progress “measured more by real tangible products such as patents, publications, and partnerships in drug discovery rather than so many forward-looking press releases.”

— JK