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NewbieWatch: BioBridge Cleans up Proteomics Analysis, Seeks Vendor Alliances


Swedish startup BioBridge wants its products to replace the software that came with your MALDI-TOF mass spectrometer. The company’s proprietary algorithms are better at reducing noise in the detection of peptide peaks and comparing the spectrum to existing protein databases, said CEO Martin Waleij.

BioBridge, established in September, now has a staff of eight, including three theoretical physicists, a molecular biologist, three programmers, and Waleij, whose background is in finance. The company will probably double in size within a year, Waleij said, with commercial programmers, user interface experts, and marketing people high on the priority list.

The initial round of financing for BioBridge was $1 million, of which 28 percent came from the Swedish venture capital firm Volito AB and the rest from the founders. Sales are already providing some income. However, the company is considering raising an additional $3 million to $5 million, and Waleij said he would soon be meeting with investment bankers in New York. “It would be an advantage if we can get a second round of financing with a US firm for more connections in the US. We want to get into the American market,” he said.

The company’s first product, PEPEX, removes higher isotopic peaks and noise from mass spectrometry data and returns mono-isotopic peaks listed with masses, intensity, width, signal-to-noise ratio, and a quality flag. AstraZeneca is an important customer, having purchased PEPEX licenses for installation worldwide. Pfizer and Aventis will soon be receiving evaluation copies, Waleij said. The package is priced at $8,000 per license, with discounts for multiple users.

Although mass spectrometers come equipped with software for peak extraction, Waleij maintained that it is “not as good” as that developed by BioBridge. “AstraZeneca was very discontented with the software that came with their hardware,” he said. In addition to the MALDI-TOF version, the software is also being rewritten for use with ESI spectrometers.

PIUMS, a protein identification tool, is designed to work on the output from PEPEX. It compares the mass spectrometry data to known proteins in databases of the users’ choice, often in-house. “We have a recipe to connect it to the database,” Waleij said. AstraZeneca has cooperated in testing PIUMS since March, and a production version is due to be delivered July 1.

The key to PIUMS’ competitive advantage is its backbone algorithm, according to Waleij. “It picks out all relevant protein candidates without giving false positives,” he said. “The scoring and validation are based on statistical models. It can say a protein is similar, but not similar enough.”

“Also, it’s fully automatic,” he added. You can go grab a cup of coffee, come back and get your results. This is a great advantage for high-throughput work. Of course, the user can go back and check that everything worked properly.”

BioBridge is marketing its software not only to pharmaceutical and biotechnology companies but also to mass spectrometer manufacturers, such as Applied Biosystems, Amersham, Bruker, Kratos, and Micromass. Initial meetings have so far yielded at least one interested hardware supplier, which Waleij declined to identify. “Our strategy is to get an alliance with one of these companies, because we make better software,” he said.

Meanwhile, BioBridge executives are considering whether to dip their toes into the complicated European patent system, or just keep everything private. With PEPEX already used all over the world, it’s too late to patent it by European rules, Waleij said. “We have the trademark, and we keep the source,” he said. However, BioBridge is considering European patent applications for the ESI version of PEPEX and for PIUMS.

In addition, protein structure alignment software developed by a BioBridge employee in collaboration with Stanford University researchers may soon be patented in the US. “You know, Stanford likes to patent things,” Waleij said. While terms between BioBridge and Stanford are still under negotiation, a license agreement has already been signed, he added.

The protein structure alignment software would be the first commercial product of its type, Waleij said. “It’s a common technique in theory, but there’s no software that really handles this problem. There are some academic packages that address it, but their hit rate is very low.” Other applications under consideration for future products include protein chip data analysis and 2D chromatography. The company has begun a collaboration with Swegene, a genomics and bioinformatics consortium including Lund University, Gothenburg University, and the Chalmers Technical Institute.


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