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Ciphergen and Applied Biosystems Offer ProteinChips for Mass Spectrometers


Ciphergen Biosystems and Applied Biosystems have signed a non-exclusive agreement to co-market Ciphergen’s ProteinChip interface with ABI’s QSTAR Pulsar mass spectrometer, Ciphergen said.

Under the agreement, ABI will offer its customers the ProteinChip interface, and Ciphergen will install and service it.

The ProteinChip interface is made up of an entry port to hold a Ciphergen ProteinChip, a translator to move it around the mass spectrometer’s vacuum chamber, as well as a laser probe and fiber optic link. The interface is attached to the mass spectrometer and allows the initial protein separation step to be performed prior to sample identification, right on the chip surface.

The interface gives you “convenience of having the separation step directly on the surface you are using for mass spec,” explained Gavin MacBeath, a research fellow at the Harvard University Center for Genomics Research. “It buys you convenience and speed in the discovery phase of a project. You’re still stuck with paying a lot for the chip and QSTAR but if you can afford it, it looks like a pretty interesting match-up.”

Ciphergen said the agreement provided a valuable addition to its protein identification product capabilities.

“Our current system has some limitations with protein identification,” said Richard Rubin, Ciphergen’s director of marketing. “Tandem mass spectrometry gets you to protein identification quicker.”

Ciphergen is discussing a similar agreement with Manchester, UK-based Micromass, in connection with Micromass’s high performance mass spectrometer, Rubin said.

Ciphergen has tested the ProteinChip interface on ABI and Micromass machines and used it internally for the past year in a contract services business for protein identification.

We’re seeing a consistent demand for this as a service,” said Christopher Pohl, Ciphergen’s vice president of research and development.

But pharmaceutical customers are more comfortable having in-house labs run the analysis, Pohl said, so the company decided to offer the interface as a mass spectrometer add-on product.

New Chips and Software

Along with the ProteinChip interface, Ciphergen has announced three additional new products this month: a new hydrophilic polymer surface ProteinChip Array, Patterns biomarker software, and a suite of application-specific protein array kits.

The chips introduce a new polymer and manufacturing process, says Pohl, offering chips that are more consistently reproducible. “It was difficult regarding consistency up to the point of the new development because every point on a chip was a polymerase reaction,” explained Pohl. “So instead, we developed a technology to create the hydrogels and attach them later, making big batches of materials stable at least for a decade. So we can make products in sufficient quantity using the same polymer every time.”

Pohl said chip batch consistency would become even more important as research moves beyond early-stage biomarker identification to large patient bases, requiring measurement of larger samples.

Ciphergen also introduced new Patterns software, which offers a numerical representation to allow the user to perform a correlation experiment directly with the software, rather than representing data as a color-coded bar chart as the earlier software did.

The new applications-specific ProteinChip Arrays kits include those for protein profiling, peptide mapping, antibody capture, and a beta-amyloid multipeptide assay for Alzheimer’s research.


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