High-Protein Diet: Genomic Solutions' ProGest Digestion Station

Genomic Solutions' ProGest Digestion Station Proteomics is just beginning to reach its potential as a major research tool. Although genomics has dominated the front pages of scientific journals and mainstream media outlets, researchers are quietly discussing the limitations of DNA and molecular biology in describing the behavior of proteins. Keith Ashman, senior research scientist at EMBL in Germany, believes that DNA-based research tools are going to naturally evolve into proteomics. "Genomics is just a linear interpretation of a protein. A gene doesn't describe how the protein interacts in a three-dimensional (3-D) environment," explains Ashman. In the early '90s, protein identification became much easier with advances in mass spectrometry. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) spectrometry and electrospray ionization tandem quadrupole (ESI/MS/MS) are two techniques that have allowed researchers to accurately identify the peptide components of a protein. "Advances in mass spectrometry have allowed proteomics to grow," comments Ashman. While mass spectrometry opened the door to protein analysis, producing peptide samples for each complex pattern of spots on 2-D gels is another bottleneck to proteomics. "It used to take us several days just to look at a few spots on a gel," notes Ashman. "We couldn't analyze a protein within a reasonable amount of time." For the past two years, Ashman and EMBL have been working with Genomic Solutions, a Michigan-based advanced biotechnology company, to assist researchers trying to manage this logistics nightmare. Their innovative solution to this problem would make Isaac Asimov proud: robots. "We know that humans make mistakes," says Lotte Downey, project manager at Genomic Solutions. "Increasing throughput and reproducibility are the advantages to our machines. What we try to do is minimize operator intervention." Genomic Solutions and EMBL have developed a new proteomics robot, the Investigator ProGest Digestion Station, just one member of a line of automated instruments used in the search for proteins in action. "An integrated, semiautomated, complete system for proteome analysis" is how Mary F. Lopez, vice president of proteomics R&D, describes the company's array of instruments. "Automation is a huge advantage," says Ashman. "With mass spectrometry and the ProGest you can quite easily work with 10, 20, 30 proteins per day. In real terms," he adds, "this is an enormous leap forward." The ProGest station is designed to automate the digestion of proteins into their peptide components. Following 1-D or 2-D gel separation, plugs are directly cut from the gel and placed in a specially designed plate capable of handling up to 96 samples. The digestion process itself is fairly straightforward. Plugs are prepared for digestion with prewashing; this is followed by a reduction and alkylation process to remove disulfide bridges, and finally application of the proper enzyme. When digestion has proceeded to desired levels, the resulting peptides are once again washed extensively and the samples are ready to be analyzed and identified via mass spectrometry, HPLC, or Edman degradation. Run time for an entire plate is just 6 hours. Apart from being time consuming, gel digestion is also an extremely delicate process that requires careful handling of samples. "There are any number of proteins on the skin that can show up in the results. It's very easy to make mistakes," notes Ashman. The ProGest station, because of several interesting design features and the creative engineering of Ashman, relieves researchers of contamination worries. An innovative contact-free injector system and valveless reactor well were developed to assure total isolation of gel samples. The injector needle, which never comes in contact with the samples, is actually two tubes, one inside the other. The inner tube handles liquids while the outer one handles gases. As liquids are dispensed into a well, the displaced air moves up and out through the outer tube. Two holes located on the bottom of every well are sealed when covered by a liquid. When the reactor chamber needs to be flushed, the inner needle is pushed upward and gases are blown out, opening the holes on the bottom of the well by disrupting the surface tension. Ashman is quick to note that previously, most researchers avoided using machines. "We started doing automation about three years ago. There was no interest at the time. People were saying that manual digestion and analysis is more precise," he says. "Now the global market is picking up on the fact that without automation, you simply can't do proteomics." Expected to be available in mid-April, the ProGest Digestion Station, along with the rest of Genomic Solutions' line of proteomic robots, is sure to be an invaluable aid in the interpretation of protein interactions. As the tide of technology flows in, all areas of science rise in sophistication. The day when researchers are replaced by fully automated counterparts may never come, but Genomic Solutions and the ProGest Digestion Station are there to make sure your coffee never gets cold. The author, Linn Cook, can be contacted at labcon@the-scientist.com. For more information, please contact the manufacturer at (800) 246-4624 or at www.genomicsolutions.com.

High-Protein Diet: Genomic Solutions' ProGest Digestion Station

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