The Australian Proteome Analysis Facility was the birthplace of the term “proteomics,” was the first government-funded proteomics center, and was the parent of the tool maker Proteome Systems — which last week began the process of filing for an IPO on the Australian Stock Exchange (see PM 6-25-04, 10-12-01). But in recent years, the facility, and Australia itself, have faded into the background as proteomics has gone global.
Now, Australian proteomics — and APAF in particular — “is back,” Mark Baker, CEO of APAF, told ProteoMonitor. Two-and-a-half years into life as a public company, APAF is “seriously trying to reclaim a strong national proteomics center,” Baker said. “Our long-term vision is to create that network where all Australian protein scientists would work together cooperatively, and where the APAF consortium would provide access to the most state-of-the-art, albeit expensive, technologies and automate the technologies.” A major part of that effort, Baker said, will be to recruit back some of the many scientists who have left APAF over the years. “I was recruited back as part of that drive 18 months ago, and the [APAF] board has been very aggressive in trying to recruit back quality proteomics scientists,” he said. Recently, Baker said, APAF has succeeded in luring back Mark Molloy, former senior principal research scientist at Pfizer, to become the director of biomedical proteomics at APAF (see p. 2). Molloy studied with Proteome Systems’ CEO Keith Williams at Macquarie University in Sydney before leaving Australia to do a post-doc in Michigan.
The center is also looking to recruit for a “few new key positions,” including director and team leader of mass spectrometry.
Baker said that the Australian government is pouring money into proteomics and other life sciences, This week, APAF won a four-year, AU$480,000 ($339,000) government grant to fund its research in high-abundance protein removal technology development. The grant, awarded by the Australian Research Council Linkage Scheme, will fund a collaborative study with Pace Farm and Qiagen on the development of APAF’s technology.
Private sector funding for Australian proteomics has, however, continued to be uneven. Last week, Proteome Systems — which initiated a hostile spin-off from APAF five years ago under Williams’ direction — quietly began the process of filing for an IPO on the Australian Stock Exchange. But the market has not been as kind as some government funding bodies have been, and Proteome Systems had to take a disappointing AU$10 million cut in the total amount it hopes to raise, in order to go through with the float (see PM 6-25-04). The company now hopes to raise AU$35 million, with a valuation of AU$160 million.
Baker said that although relations between APAF and Proteome Systems have been strained ever since the spin-off occurred, “it has been one of my priorities to reestablish a strong, vibrant, healthy, cooperative relationship with [the company],” and that “we’re watching very keenly what happens with [Proteome Systems] in terms of where they go as an Australian company, and we do wish them well.”
Back to Protein Chips
Before returning to APAF, Baker was director of R&D at another hostile spin-off: LumiCyte, a Fremont, Calif.-based spin-off of Ciphergen founded by former Ciphergen chief scientific officer, William Hutchins, in 1999. In 2003, LumiCyte and Ciphergen settled a prolonged dispute over the rights to SELDI-based products, with Ciphergen forking over $3 million in cash and 1.25 million shares of Ciphergen stock to LumiCyte in exchange for exclusive rights to SELDI technologies (see PM 6-6-03).
Meanwhile, LumiCyte — which now calls itself LCI — has been busy developing, in collaboration with Baker, a new set of protein chips that it says have superior sensitivity and versatility compared with SELDI. The chips can interface with any mass spec, and Waters and Thermo Electron have agreed to co-market them with their mass specs. “Initially we’re doing [this] in a joint marketing agreement, but ultimately it may be something that LumiCyte does,” Christopher Belisle, vice president of biochip technologies at LCI, told ProteoMonitor.
Belisle said that initially two chips will be available for sale: a targeting and concentration chip for concentrating samples prior to MALDI-type MS analysis, and a reverse phase chip for interfacing with 2D gels or LC. In the next three to six months, LCI will also release a customizable antibody chip, and an IMAC chip is also in the works, Belisle said. “This platform can also be used in a combinatorial approach, so unlike SELDI, where a sample gets exposed to a chip and whatever binds, that’s what you analyze — in our platform, the serial exposure of a particular sample droplet across multiple different types of surfaces can be done,” he said.
Baker is currently testing the chips for use with APAF’s Applied Biosystems 4700 mass spec, and said that “APAF is negotiating a position where it will get access to the technology first.”
APAF is also in the process of developing a system for high-abundance protein depletion that Baker says “will be able to drill significantly more deeply into the proteome” than existing technologies, including Agilent’s Multiple Affinity Removal System (see PM 8-18-03). “The difference is that 10 percent or 20 percent is not enough — you’ve got to really be drilling down into the 99.9 percent of protein removal in order to see biomarkers,” he said. APAF is filing for patents surrounding its protein removal system.
In addition, the facility is concentrating on developing technology in the areas of gel imaging, fluorescence labeling, signal transduction pathways, and post-translational modifications, Baker said. He hopes that in the next few years, APAF will be able to create and distribute IP surrounding these technologies, and stake a hold in at least two industries: plant directed evolution, and personalized medicine.
In the short term, Baker is just hoping for a little more attention to turn back to the down-under side of proteomics. “We are a major international research facility, so our doors are open. If [people] have ideas or technology they want to try out here, if they wanted to cooperate with us, we’re very open,” he said.