At A Glance
Name: Ben Herbert
Position: Executive vice president and head of array technology, Proteome Systems
Prior Experience: Developed 2D gel analysis techniques for studying wool proteins, taught 2D gel electrophoresis course at Macquarie University under Keith Williams
How did you become involved in proteomics?
I’ve been doing proteomics for about 17 years, since before the word had even been invented. I’m from New Zealand originally, and I left high school and went directly to work in a lab for the New Zealand government science organization, which is similar to the NIH. The government funds a lot of the big science in New Zealand, although nothing in New Zealand is particularly big!
I didn’t go directly to University and do a full-time degree; I wasn’t really that sure what I wanted to do when I left school so I went to work. I just was incredibly lucky: I walked into a chemistry lab, and there was a PhD protein chemist who wanted to use isoelectric focusing to identify different species of meat and fish. This organization [where I worked] was meant to check all the food products being sold in New Zealand to make sure [a particular piece of fish was actually what people said it was]. The chemist knew how to run an isoelectric focusing gel but he wasn’t incredibly expert at it and he needed a technician. He got me. I was 17 years old, straight out of high school and I had no idea what a protein was. I started running gels, got interested in it, and started to read lots of literature on it. I was studying part-time [for an undergraduate degree], and I’ve been running gels and 2D gels ever since.
So where did you go from there?
That was way back in 1986. I spent 5 years there, and then I moved to the Wool Research Organization of New Zealand. Because wool is such a massive industry in New Zealand there’s a whole research outfit funded by the wool industry. They were interested in looking at proteins because wool and hair are made of proteins, and they were interested in looking at how those affected the final properties of the fiber — things like fiber strength, color, curliness of the fiber. I worked there for 5 years, but New Zealand was a fairly isolated type of place. There weren’t very many people doing protein electrophoresis, especially 2D protein electrophoresis. When Pharmacia first released the IPG technology, I bought the first apparatus sold by Pharmacia in New Zealand. Everything I did I just taught myself. I read the literature and just experimented. In those days milestones were unheard of — you just got the money and off you went. You could play and do all sorts of interesting things. But it was very isolated as well.
How did you hook up with Keith Williams and Proteome Systems?
I looked over to Australia to see what was around there, and just by pure luck I met Keith Williams and the guys at Macquarie University, who for an academic group were quite commercially focused. They ran training courses on electrophoresis in association with companies like Pharmacia. I came over to Australia and went to this training course — really just to try to meet people — and I met Keith Williams, Andrew Gooley, and a whole bunch of people who became the founders of Proteome Systems. I told them what I did, and they were all quite amazed that not only could you extract proteins out of something like wool, that you could run a 2D gel of them as well.
I ended up getting invited to come to Australia and teach the first 2D gel course that they ran at Macquarie University. I got to know the group, and by 1995 they were in the final stages of getting the Australian government to fund what became the Australian Proteome Analysis Facility at Macquarie University. The only part for which they didn’t have any expertise in-house was 2D gels, so Keith invited me to come over from New Zealand.
I’d been working as a researcher for 10 years but I’d still not done a PhD. I’d basically been too disorganized and lazy to go to University full-time, give up a salary, and get a PhD. Keith offered me this amazing opportunity to be involved in starting up this proteomics facility and do a PhD at the same time. So it was a fantastic opportunity. Suddenly there were all these people who were incredibly interested in 2D gels, whereas back in New Zealand they were kind of a curiosity. But suddenly when proteomics took off, and it took off enormously in Australia, everybody wanted people who could run 2D gels. It was a fantastic time.
How did you go about getting your PhD?
The thesis title was “Advances in Two-dimensional Electrophoresis for Proteome Projects.” It was all about [wool] because I started working on wool, but there were two themes in the PhD. One was solubility and looking at better ways to resolve proteins on gels. The other theme was instrumentation, and how we could make better, more user-friendly types of instruments to run 2D gels. Now, 7-8 years down the track, I’m still working on the same things; it’s just iterations of that, looking at improvements in the instrumentation — how to make 2D gels easier to run, and how to do sample prep in a high-throughput, reproducible fashion to get better solubility. All those things are still important issues for proteomics, and especially for 2D gels.
Has the debate over the relative merits of 2D gels versus multidimensional chromatography mellowed at all?
I think there’s more acceptance that 2D gels have their place, and that they provide information that’s very difficult to get any other way. Part of what’s driven that is the realization from the sequencing of the human genome that there aren’t that many genes, so people want to know where the complexity really comes from! The complexity seems to come predominantly from post-translational or co-translational modifications that are very difficult to pick up through genomics, and they’re very difficult to pick up with anything that doesn’t resolve proteins by isoelectric point. There’s no really solid way of doing that except by isoelectric focusing. So if you want to find out how many isoforms there are of a protein, resolve them, and study each one separately, you really need 2D gels to do it. So people are saying now, ’Well OK, they do have a place.’
I was just at the Siena proteomics meeting and I saw presentations where people had done quite substantial studies using both an LC/MS and a 2D/MS strategy, and they were saying that a fairly large proportion of proteins — about 40 percent of the proteins that they got on the 2D gels — didn’t show up in an LC/MS strategy. That’s quite interesting. What it’s saying is that the two techniques are probably quite complementary. You’re not going to be able to get away with just one or the other; you really need both. That’s the nature of proteomics. It’s a tremendously complex sort of science, and I don’t believe there will be one particular technology that will come to dominate completely.
Are there other challenges that you are addressing in your group?
People have been working on this for quite a long time, but the big thing that’s looming for me is working under native conditions, and looking at protein complexes rather than just denaturing everything and looking at individual proteins. If you look at all the electrophoresis techniques, like isoelectric focusing and normal electrophoresis, they were all invented and used under native conditions before they were ever used under denaturing conditions. There’s no fundamental reason why we can’t use them [that way now]. Isoelectric focusing still resolves modified forms of proteins under native conditions the same as it does under denaturing conditions.
The other big thing that we’re starting to work on is organelle fractionation. To get organelles out of a cell, you really have to be quite careful in how you break the cell, otherwise you’ll break all the organelles as well. It’s a whole new type of sample prep, but in reality all of these methods have been around in biology and biochemistry for decades. People just need to look in the literature and adapt the methods that already exist for proteomics, and look at them and say, ’How can I make this easier? How can I do it on 100 samples at once instead of one sample?’ But I still think there’s more to be done with conventional 2D gels under denaturing conditions. I’m not convinced that we’ve reached the end of the road there either. I think we can do better in terms of solubility. We’ve got some patents that we’ve filed on increasing solubility using different sorts of sample solutions. I think we can make some improvements on the current state-of-the-art there as well.
Have you experienced reluctance on the part of big pharma towards committing resources to proteomics partnerships?
I guess it’s true that big pharma has been a little bit maybe gun shy towards working with proteomics companies, and maybe that stems at least partly from getting in early with some of the really early proteomics companies, when the technology was still very immature. I’m not sure a lot of the results from those early studies were fantastic. And I’m not aware of any pharma companies that don’t have their own in-house proteomics efforts. But in talking to them I think they’re finding that there’s so many different disciplines in proteomics that they really need to outsource some aspects of it as well — get some external groups to help them with things. So it becomes a collaborative effort rather than just handing off an entire project to an outside group. That’s really where our discussions have been.
On the other hand we’ve also begun to fund a lot of our own in-house discovery projects, because then we’re totally in control and we own all the intellectual property. We’re running multiple strategies at once. I don’t think we can afford to focus on just a single strategy and say we’re going to partner with pharmaceutical companies, because you’re fairly exposed if it doesn’t work very well.