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PROTEOMICS 2D Gel Automation Next Goal for Instrument Makers

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Automation comes slowly in the world of 2D gel electrophoresis. As most proteomics researchers know, 2D gels are far from hands-off — and far from headache-free. But several companies are now attempting to automate the post-separation sample purification and transfer steps associated with preparing proteins for a mass spec. The goal: less busywork for bench scientists, and more low-abundance peptides in their results.

One of the first entrants to this market comes from Millipore and Applied Biosystems, a collaboration formed in 2000 to design new instrumentation for proteomics. Their device, the ZipPlate, adapts Millipore’s popular ZipTip pipette tips for a 96-well plate format and provides a protocol for combining in-gel protein digestion with the spotting of the purified and concentrated peptides onto a sample target for MALDI mass spectrometry.

By automating the de-staining, digestion, concentration, desalting, and spotting steps, the ZipPlate should in theory allow scientists to identify low-abundance proteins that might otherwise have been lost during sample handling. “For every single manipulation you do, on a good day you can lose 10 percent, on a bad day 40 or 50 percent, so cutting two manipulations out may improve your yield by 50 percent or more,” says Keith Ashman, director of mass spectrometry at the Samuel Lunenfeld Research Institute, who beta-tested the ZipPlate.

Gyros, a Swedish spinoff of Amersham Biosciences, says it’s working to integrate in-gel digestion into its own automated platform, which spins individual samples through channels etched in a compact disc that doubles as a MALDI target. “We’re planning to hopefully present something in late spring next year where we show more results around this,” says Per Sjöberg, Gyros’ executive vice president for commercial operations.

Even Amersham has made strides toward automating spots excised from 2D gels. This fall, Amersham began offering a spot-handling workstation that integrates picking, digestion, and spotting.

While Sjöberg says Gyros had not determined a list price for its CD-based platform, Rick Garretson, Millipore’s proteomics market development manager, says using the ZipPlate would reduce by half the cost per sample of performing the equivalent analysis with ZipTips.

— John S. MacNeil

 

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