By Mark D. Uehling
June 17, 2004 | Is production-scale proteomics ready for mere mortals who don't work for billion-dollar pharma companies? The answer, in Oregon, is yes.
The Oregon Health & Science University is the state's main academic medical center, with two hospitals that treat 187,000 patients a year. It's also a major research site, with 1,500 scientists -- and a new $1-million core lab for proteomics. Cory Bystrom, director of the Proteomics Shared Resource, had to purchase his tools carefully: He has a small budget and a staff of one technician.
"We've got so many types of samples and workflows and strategies and concepts to try to deal with," says Bystrom, a chemist. "At the end of the day, we're just trying to manage the data -- keep track of what we've done and how we've reached the conclusion."
Some components of the Oregon proteomics facility include the Fuji FLA-5000 Fluoroimager (gel imager); Applied Biosystems QStar XL (electrospray or MALDI mass spectrometer); Eksigent nanoLC (HP liquid chromatography system); Mascot (protein identification software); Phoretix 2D Evolution (protein-expression analysis software); and ProID and ProICAT (database searching, protein expression analysis software from Applied Biosystems).
One slightly more novel piece of the puzzle is the Proteus laboratory information management system (LIMS) from GenoLogics, a Canadian company. Says Bystrom: "We've been beta-testing the LIMS. I was scared at first. But we're having very good results. It's matured very rapidly to the point where I think we're going to try very hard to move the LIMS into production in the next several months, on a routine basis, for managing all our sample tracking."
Managing not only the raw data but also the metadata about the gels, he says, would be unwieldy in a paper notebook or computer spreadsheet. "The data is really the most important part of everything that's happening," says Bystrom. "If we don't have a good way to manage the data and deliver it quickly, we would find ourselves struggling."
In British Columbia, GenoLogics president and CEO, James DeGreef, says the 12-employee company's LIMS has been designed around managing proteomic data. "Our focus in LIMS is on proteomics," he says. Instrument vendors, he says, tend to price their LIMS between $200,000-$300,000, which is outside the range of many government and academic customers. GenoLogics' price: $80,000. Even after extensive customization of competitors' tools, he says, some customers don't feel that generic LIMS are as tailored to proteomic workflows as they need to be.
Bystrom also invested in the 2DiDX spot-cutting robot from Leap Technologies. "One of the reasons we selected that is because of the very high quality design of the robot," says Bystrom. "This robot has got a sensor built into the cutting head to make sure the gel plug is successfully removed from the gel we're trying to take the sample from. That's probably been the weak link in previous generations of instruments."
The Leap robot also exports data about its efforts in XML format, helping Bystrom keep track of projects. "That's become the next-generation standard for data-manipulation management," says Bystrom. "It keeps track of the spots it was supposed to cut, the spots it successfully cut. Even something that sounds so simple -- keeping track of the samples that have been removed from a gel, what microtiter plate they've been put into, and what are you going to do with that microtiter plate later -- is an important part of the whole sample tracking exercise."
Bystrom declines to discuss the lab's turnaround time or throughput. "We've only been open a couple of months," he says. "We're working out a lot of bumps. We're trying to strike a balance between performance and reliability."
Still, it's clear from the lab's pricing sheet -- $150 for a full-service MALDI identification of a protein, with a 15 percent discount for more than 24 spots -- that the lab will try to provide economies of scale. It's also clear that the data are paramount, with every project's output currently etched on CD-ROM or DVD, but soon to be available via the Web as well.