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PerkinElmer and Beckman Expand Into Proteomics With Mass Spec, Arrays

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Among proteomics specialists, PerkinElmer is not the first name that comes to mind. Neither is Beckman Coulter. But these large life sciences instrument companies want to change this perception.

“We’ve been dabbling in proteomics for quite a while,” said Sandra Rasmussen, leader of the proteomics business unit at PerkinElmer. “But key components were missing.” PerkinElmer has now filled in the gaps with instruments from Packard, which it acquired in late 2001; Genomic Solutions, whose instruments it is now selling under its own brand; as well as a new mass spectrometer jointly developed with MDS Sciex of Toronto.

At the Lab Automation 2003 conference in Palm Springs last week, the company turned out in force to promote its full line of proteomics products, including its ProXpress Proteomic Imaging System, Progenesis 2-D image analysis software, ProXcision gel cutting robot, which is slated for commercial launch in May, and MultiProbe II proteomics workstation for in-gel digestion and spotting. At the conference, PerkinElmer launched its new prOTOF 2000 mass spectrometer.

The instrument, which will sell for $350,000 to $365,000, is a MALDI-TOF mass spectrometer in which the time-of-flight path is orthogonal to the sample, similar to an orthogonal ion source available for ABI’s QSTAR, also developed in collaboration with Sciex. This design supposedly improves mass accuracy and resolution, as well as the stability of calibration.

Rasmussen said the prOTOF has achieved a resolution of greater than 10,000 for peptides of 500 to 3,000 Daltons, and mass accuracy as low as 2-3 ppm over the same range. In terms of sensitivity, the company has been able to detect peptides down to one femtomole. The design of the system also eliminates the need for internal calibrants, she said, preventing ion suppression.

Instead, an hourly external calibration is sufficient. In addition to stainless steel target plates, 96-, 384-, and 1,536-well disposable sample plates that sell for $75-$150 are also available. The disposable option is intended for users afraid of contaminating their sample plates, or those who want to store them for future analysis.

But most importantly, will the new mass spec help users get better protein identifications? PerkinElmer claims it will, but provided no data to back this up. Both mass accuracy and sensitivity play a role in peptide mass fingerprinting, according to John Cottrell, co-founder of Matrix Science, which provides Mascot. The principal benefit of an increase in resolution is “a reduction in the scores for random matches,” he commented.

According to Ron Beavis of the University of Chicago, the prototype of the instrument was actually developed in the labs of Ken Standing and Werner Ens at the University of Manitoba in Canada. The instrument’s main advantage, he believes, is its ease of use that will allow for automation and consistent results across different users. “You don’t have to be an expert to run the machine,” he said. However, it may not be its mass accuracy and resolution that set it apart from competitors, such as Bruker’s Ultraflex, which sells for $360,000, or ABI’s Voyager-DE STR, listed at $334,000. “If you have a trained operator, using either of those machines you can achieve that sort of resolution and mass accuracy, but it takes quite a bit of effort,” Beavis said.

PerkinElmer’s new instrument will come with software that includes algorithms Beavis developed: The software package will feature the peak picking algorithm m/z and the Profound search engine, though customers are free to use their own search engine.

This month, PerkinElmer will begin beta testing the prOTOF, and is still signing up users for this program. A full commercial roll-out is slated for May, when PerkinElmer also wants to introduce its ProXcision robot. A LIMS to integrate all of the instruments is in the works.

Ole Jensen, an associate professor at the University of Southern Denmark in Odense, tested a “breadboard” version of the proTOF for a day last November and concluded that “its main advantage is the high peptide mass accuracy that is easily obtained by external calibration,” which saves significant time during analysis. “The overall performance was very similar to existing high-end conventional axial MALDI-TOF instruments,” he said.

Beckman Bets on Proteomics, Too

Beckman Coulter, which like PerkinElmer had a strong presence at the Lab Automation exhibition hall, seems to be pursuing a similar strategy to its east coast competitor: branding and re-branding. Early this year, the company started a “ProteomeLab” marketing initiative that “brings the company’s life sciences technologies together to address current challenges in proteomics,” according to a company statement. Under the ProteomeLab brand name, Beckman is pulling together a variety of instruments, reagents, and software of relevance to proteomics, some of which are modifications of existing systems.

As part of the new package, Beckman launched two new products last month: The first is a capillary electrophoresis system called PA-800, which can be used to determine a protein’s molecular weight, perform isoelectric focusing, or separate peptides. The second is a two-dimensional chromatographic protein fractionation system called PF-2D that resolves proteins by isoelectric point in the first dimension and by hydrophobicity in the second dimension.

At the recent CHI PepTalk meeting in San Diego, John Hobbs, Beckman’s strategic marketing manager, gave a glimpse of a product the company is planning to roll out this spring: protein microarrays. With these, the company will step into a proteomics field that is getting more crowded by the week — Zyomyx, for example, launched its protein biochip platform last week. But Beckman’s arrays will be unique. According to Hobbs, the format will be a microtiter plate, with up to 100 features per well. Each well will be studded with oligonucleotide linkers, to which the proteins will be attached via complementary oligos. According to company officials, the first protein chips will be custom arrays, followed by a cytokine detection array later this year.

Whether jumping on the proteomics train will actually help the two companies boost their revenues remains to be seen — but it appears both are optimistic that researchers in the field will have resources to spend for some time to come.

— JK/MMJ