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Q&A with Keith Williams, CEO of Proteome Systems

NEW YORK, Dec 6 – Over the past few months proteomics has taken center stage within the genomics sector and no-one could be more excited about the buzz than Keith Williams, president and CEO of Australian start-up Proteome Systems.

As a founder of the Australian Proteome Analysis Facility and a co-editor of Proteome Research: New Frontiers in Functional Genomics , one of the first books published on the subject, Williams was among the earlier movers in the industry.  

Earlier this week his 60-person company said it would extend its alliance with Shimadzu by jointly establishing two proteomics facilities in Sydney, Australia and Boston, further strengthening Proteome Systems' position in the nascent sector.

GenomeWeb recently caught up with Williams to discuss his company’s relationship with Shimadzu as well as his strategy for establishing Proteome Systems as a leading proteomics player.

GW : Can you tell me about the facilities you have planned in partnership with Shimadzu?

Williams : The initial relationship with Shimadzu commenced around our Chemical Printer instrumentation. That involves a partnership with MicroFab Technologies. We’re building the Chemical Printer in partnership with Shimadzu. We have prototypes of the instrument and it will be implemented in our discovery programs in the first quarter of next year.

We’re still thinking about when we’ll sell it because it’s a fairly new instrument and we want to make sure we’ve got the bugs out before we commercialize it. But it will be given a pretty hard test drive in our discovery program.

The other instrument we’re building with Shimadzu is a gel-cutter liquid handling system. Its code name for the moment is Xcise. At the moment, surprisingly enough, in terms of conventional technology - running gels, excising samples, doing liquid handling and putting them onto a molding plate - there’s no instrument that does all of those processes in one go. We see the opportunity for an instrument there.

We’re actually going to manufacture that here in Sydney and Shimadzu’s going to market it. And from that, we’re discussing a number of other instruments with Shimadzu.

GW : How are you positioned in the Japanese proteomics market?

Williams : Certainly we feel now we’re going into Japan as an insider. I think that’s going to help with partnerships with big pharma in Japan. We’re seeing some signs of that already. Because of the way Japanese industry works… we [now] have the opportunity to get introductions to different groups in Japan through our Shimadzu connection.

GW : How would you describe Proteome Systems’ business model?

Williams : Basically I guess our company has two sides. One is a technology development side because the instrumentation in proteomics isn’t satisfactory at the moment. And the other side of the business is to do discovery, to be a Celera- or GeneProt-type company in terms of looking at disease and building databases. We now feel confident that we can begin to scale up that process, so we’ve been partnering with Shimadzu in relation to beginning that process.

GW : Are you modeling yourself after Celera?

Williams : The informatics is almost a byproduct of our business rather than being the center plank. We don’t really understand how to value the informatics side. So what we’re more focused on is being a discovery company rather than an informatics company. But in terms of what we’ll do, the grunt work of screening through tissue samples, we’re in competition with Celera and GeneProt in that sort of activity.

We like to think that we’ve got a very novel technology platform that will underpin that.

GW : Are you planning on licensing your database?

Williams : We feel a little unclear about how to commercialize that at the moment. We’re certainly beginning to build some very substantial databases. We’ve also learned a lot about how to add value to EST databases. We take genomics databases and make sense of them.

There are a lot of similarities to Celera, but we may use the databases primarily in discovery rather than selling them directly. That will evolve with time.

GW : So you see that as being the next step for you?

Williams : Yes. It’s not central to our business model, though. Celera sort of lives and dies on its informatics and we’ve sort of made the decision that we’ll live and die on some other things.

GW : Do you have an advantage over competitors that are basing their proteomics programs on what worked for genomics?

Williams : Our view of chips is a genuine protein chip rather than an attempt to reinvent a DNA chip into a protein chip, which in our view is problematic.

I think what’s really important is that we see the different forms of the protein. If you’re thinking about antibody chips, conventionally you’ll put the antibody to protein X down on your array, and all of the different forms are likely to bind to that antibody. So, again, it’s not informational. You don’t get information about the exact form of the protein.

We think these are important distinctions and that, in people’s rush to be high-throughput, there’s not a lot of thought very often into exactly what they’re doing.

GW : Is Proteome Systems doing any work on antibody microarrays?

Williams : I think a number of groups are working on antibody arrays. Our approach has been more to come from the protein side. We’re certainly in the process of building an instrument that can print antibodies onto each of the proteins that we array.

Whereas our competition is mostly thinking about putting antibodies down in ordered arrays to then add tissue samples to find what the proteins are in that sample, our approach is a little bit the other way. We array our proteins and then use antibodies to identify reactivity.  

Our focus is on arraying authentic proteins and I think we may be one of the only groups that’s focusing on that at the moment. Lots of other groups, if they’re putting proteins down, are working with recombinant proteins and we have question marks about what that means. We don’t think it’s like DNA.

I would be extremely skeptical if recombinant proteins were authentic. It may be true for some soluble proteins. People are very, very cavalier about what they mean by recombinant protein at the moment because I don’t think it’s often clear what the authentic protein is.

GW : What’s next for Proteome Systems?

Williams : What we’re looking to do is package up the whole process so I guess “systems” in the name of the company is significant. We see this as a systems issue and we’re building a platform that we think works.

There are a lot of both instruments and consumables and kits being developed at the moment and there will be a rollout through 2001 of individual items but also we’ll be packaging that up into a kit.

We think the instruments and consumables is a very interesting emerging business and will provide us with substantial cash flow, which will help us be able to fund some of our own discovery and informatics programs.

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