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Biognosys Closes Series C Round, Plans to Open US Office


NEW YORK (GenomeWeb) – Swiss proteomics firm Biognosys said today that it has closed a Series C financing round with which it will continue development of its data-independent acquisition mass spec offerings and open a US office.

Biognosys plans to open an office in Boston toward the end of the first quarter of this year, CEO Oliver Rinner told GenomeWeb. The company did not disclose the amount raised in the Series C round or the participating investors, but said the round generated in the "mid-single-digit millions" of dollars.

Biognosys will keep all of its mass spec facilities at its headquarters outside Zurich, while using the Boston office primarily for US business development and the initial processing of some samples for its US customers, Rinner said.

He noted that the company, which was founded in 2008 as a spinout from the lab of Swiss Federal Institute of Technology researcher Ruedi Aebersold, has, for around the last three years, done the majority of its business in the US, finding solid demand for its DIA mass spec services among early-stage biotech firms.

"We work with pharma, certainly, but also with many venture-financed biotech companies," he said. "Boston and the West Coast are home to many [such] biotech companies [that] are especially open to new technology for their research."

The recent financing follows a Series B round of an undisclosed amount that the company closed in 2012 and a CHF2.7 million ($2.7 million) Series A round in 2011 that drew investors including Redalpine Capital and Syngenta Ventures.

At its launch, Biognosys was focused primarily on offering mass spec-based targeted proteomics services such as multiple-reaction monitoring assays, including a number of MRM assay panels tailored to specific research interests. More recently, the company has come to focus on its Hyper Reaction Monitoring mass spec approach, a Swath-based DIA method that it offers as a service mainly for discovery work and large-scale protein quantitation.

Rinner said the company has drawn a diverse range of US clients, including agricultural companies, pharma firms, and biotechs. Their work is focused on "primarily early discovery questions," he said. "Like with a drug you want to know in cell culture what happens in the total proteome level."

The main rationale for opening the Boston office is to be closer to the company's US clients, Rinner said, but, he added, that in the case of certain kinds of samples, it will be helpful to have a US location where some initial processing can be done before they are sent to Switzerland for mass spec analysis.

Biognosys also plans to use the Series C funding for further technology development, Rinner said, noting that there are a number of portions of the DIA process where improvements could be made.

For instance, improved chromatography, which could provide smaller and more intense peaks could provide "large gains," he said. Additionally, he noted, improvements on the instrumentation side open up new possibilities on the bioinformatics side.

"If you have higher resolution and can get better mass accuracy and [can], for instance, better deconvolute isotopes, then this allows you to use new algorithms," Rinner said.

He added that the company is also interested in improving throughput and exploring new variations on the DIA technology.

"So far we are mainly using long gradients and long injection times to really increase depth [of coverage], but now we have developed the potential to increase the throughput to go into the hundreds of samples, which is very interesting for some applications," he said.

DIA workflows that don't require use of a spectral library for making peptide IDs are also of interest, Rinner said.

DIA's use of broad m/z windows presents a challenge in that fragmenting all the ions in these windows results in very complicated spectra with considerable noise as the precursors captured in these windows interfere with one another. To get around this, DIA analyses have typically employed a targeted approach to identifying and quantifying peptides akin to the process used in multiple-reaction monitoring mass spec.

This approach requires that researchers first generate a spectral library for their sample using a conventional DDA run. They can then search data from subsequent DIA runs in a targeted manner against this spectral library.

Recently, however, some researchers have begun exploring methods of analyzing DIA data that don't rely on spectral libraries. For instance, last year, the lab of University of Michigan researcher Alexey Nesvizhskii published a paper in Nature Methods presenting an informatics package called DIA-Umpire that allows users to generate pseudo-tandem MS spectra from DIA data, enabling conventional database searching and the generation of spectral libraries without the need for a separate data-dependent acquisition run.

In November, researchers at the University of California, San Diego put out another algorithm, named MSPLIT-DIA, for untargeted analysis of DIA data.

And last month, researchers at the Institute for Systems Biology published a method that uses Swath to analyze protein post-translational modifications and can detect PTMs not present in the spectral library used for the initial data analysis.

"At the moment there is no question that a really good spectral library to your target sample gives you the best data, but on the other hand I think that for some occasions it could make sense, especially with modifications, not to rely on having the library" Rinner said. He added that that Biognosys was collaborating with a variety of groups on new DIA workflows.

He noted that, using its standard HRM approach, Biognosys has been able to reproducibly quantify as many as 8,000 proteins in a single run.

"And once you go beyond that, then you are getting into something really interesting," Rinner added. "Because [based on previous studies] you expect around 12,000 proteins at a time to be expressed in a given cell type. So suddenly you are not too far away from seeing the whole expressed proteome. And that means you have a total view of what is going on in the cell very similar to RNA expression."