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Biognosys Seeing Growing Pharma Demand for Swath-based Protein Quantitation Services

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NEW YORK(GenomeWeb) – With sales growing at a double-digit clip, Swiss proteomics firm Biognosys is carving out a market for its mass spec-based protein quantitation services.

This year, the company, which specializes in development of multiple-reaction monitoring and data independent acquisition mass spec assays, will report roughly CHF 2 million ($2.1 million) in revenues, up 50 percent from around CHF $1.3 million in 2013, CEO Oliver Rinner told GenomeWeb.

Pharma has proven a particularly strong market for the company's services, Rinner said, noting that while proteomics has traditionally focused heavily on biomarker discovery and development, a number of drug makers have found Biognosys' assays useful for target deconvolution and investigations into the proteome-wide effect of drug treatments.

Last week, the firm announced it inked a deal with AstraZeneca for use of its Proteome-SEQ service, a DIA mass spec-based approach that enables reproducible quantitation of thousands of proteins across multiple samples.

In DIA, the mass spec selects broad m/z windows and fragments all precursors in that window, allowing the machine to collect MS/MS spectra on all ions in a sample. This means that, unlike in conventional shotgun proteomics, the same set of ions are measured each time, allowing for more reproducible quantitation across samples – a key for quantitative studies. 

DIA has seen a significant growth in popularity since AB Sciex's 2011 launch of its Swath method, developed in collaboration with Swiss Federal Institute of Technology Zurich researcher Ruedi Aebersold, one of Biognosys' co-founders and a member of the company's advisory board.

However, according to Rinner, Biognosys is currently the only company offering DIA mass spec as a commercial service. 

"[DIA] has been around for a while, but we are the only commercial provider," he said, adding that the intensive data processing required for the method is perhaps one of the reasons other firms have yet to jump into the fray.

As a spinout of Aebersold's lab, company founders were involved in the original development of the Swath technology, which, Rinner suggested, has given the firm an advantage in terms of bringing DIA-based services to market. 

He noted that convincing customers to take a chance on a relatively new proteomic technology presents certain challenges, but that Biognosys has found opportunities in companies left dissatisfied by more traditional approaches like standard shotgun mass spec or affinity-based methods. 

"Often times people come to us who have tried other technologies like shotgun proteomics or Somalogic's [SomaScan service] or any other protein expression technology," Rinner said. "And the main argument we make to convince them is really the quality of the data."

"We can tell them that [the approach provides] gapless data matrices, data that are very reproducible," he said. "They find this a really compelling offering. They hate noisy data because it's not actionable."

In an interview with GenomeWeb last month, Somalogic CEO Byron Hewett said the company's SOMAscan platform is on pace to generate around $20 million in revenues this year. In citing the platform as a competitor, Rinner noted that while SOMAscan can offer higher throughput, Biognosys highlights the level of certainty provided by mass spec compared to affinity-based methods.

"It is specificity," he said. "It is hard for affinity-based methods to really prove that what you think you are measuring is what you are really measuring. And that is what customers have told us when they cross-compare both methods."

He added that another potential advantage is the relative ease of generating new mass spec assays to proteins in uncommon sample types.

"We look at human, but we also look at unusual samples from unusual organisms in the plant field," Rinner said. "These are areas where no [affinity] reagents are available, so the mass spec has an advantage there."

Biognosys currently offers two standardized panels through the Proteome-Seq service: a cell culture-based panel that can quantify more than 4,000 proteins in cell cultures from 20 µg of protein; and a human liver panel that can quantify more than 2,000 proteins from 5 mg of fresh frozen tissue.

The company is working on several additions, including a human plasma panel and a mouse liver panel, that it plans to launch next year, Rinner said.

The company also does custom Swath-based work on a variety of sample types, he added. The approach can work with as little as 10 µg of sample, with mass spec analysis taking roughly two hours per sample, he said.

Rinner said that the company had been somewhat surprised at how much demand thus far had come from pharma firms for drug development work as opposed to traditional biomarker discovery research.

"I think more and more in the drug area people are looking at target deconvolution and want to see how the whole proteome reacts [to an agent], not only the isolated drug targets," he said.

The company has also drawn customers from applied markets like agricultural research, where people are interested in studying how, for instance, an herbicide may perturb the overall proteome of a plant, Rinner added.

While Aebersold's lab largely used AB Sciex TripleTOF 5600 instruments for its Swath development work, Biognosys uses Thermo Fisher Scientific's Q Exactive for its Proteome-Seq service. Rinner said that the approach worked well on both the AB Sciex and Thermo Fisher instruments, with the two systems giving "very comparable data."

Unlike many proteomics firms, Biognosys has no biomarker development programs of its own and no plans to launch any in the immediate future, Rinner said. 

"Our focus is really on providing the tools and solutions for protein research," he said. In addition to protein quantitation services, the company sells its Spectronaut software for analysis of high-resolution quantitative data, as well as kits including its multiple-reaction monitoring mass spec PlasmaDeepDive MRM Panel, which, according to the company, allows for quantitation of 100 human plasma proteins across six orders of dynamic range.

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