A new proteomics services firm has opened its doors in northeast England with the goal of reaching small- to mid-sized pharmaceutical and biotech firms who have been unable to access proteomics tools and technologies.
The North East Proteome Analysis Facility, or NEPAF, located in Newcastle-upon-Tyne, came online late last month, one year after securing £4 million ($5.98 million) in funding from the regional development agency One North East and the European Regional Development Fund as part of a wider economic development effort in the region.
While proteomics-service companies on both sides of the Atlantic have faced difficult times recently, the new facility debuted after a second regional development agency in northeast England called Cels identified the need for such a firm in the small- to mid-sized pharma and biotech market.
According to Glen Kemp, program manager for NEPAF, proteomics has historically been a field open only to deep-pocketed big pharma and research groups, while smaller players have been left to watch from the sidelines.
“They basically can’t even afford to buy the equipment or to dedicate the resources and staff to really get to know the equipment and get the most out of it,” Kemp told ProteoMonitor. “So for a lot of those small- or medium-sized enterprises, there’s a big barrier [to] entry.”
Housed in two locations, Newcastle University and Durham University, NEPAF offers the basic services that would be expected from a proteomics service firm, including biomarker discovery and validation, protein analysis, and de novo sequencing.
NEPAF, which is not a core facility, is equipped with five mass spectrometers, 1D and 2D gel electrophoresis platforms, PAGE scanning and image-analysis equipment, a nano-liquid chromatography system, and a reverse protein-array system.
Though it officially launched in October, NEPAF’s laboratory has been up and running since July, and since then it has been doing work for several undisclosed clients, Kemp said. NEPAF, he added, is aiming to generate enough revenues by the end of next year to become self-sufficient.
Rising from the Ashes?
The facility made its debut at a time when an ongoing shake-out in proteomics has hit proteomic-service businesses especially hard. Indeed, some would consider it paradoxical that Cels pushed to create NEPAF as part of a broader initiative to expand North East England’s economy by establishing and growing a healthcare and life-science industry in the region.
Not long ago, such proteomics service companies were the rage when proteomics was being sold as the magic bullet that would lead to transformative treatments, even cures, for diseases such as cancer and Alzheimer’s, but more recently such companies have been forced to retreat amid skepticism about the utility of proteomics in general.
“They basically can’t even afford to buy the equipment or to dedicate the resources and staff to really get to know the equipment and get the most out of it.”
The science turned out to be more difficult than people had imagined, and meaningful data with clinical relevance was further off in the distance than anyone wanted to see. Companies including Geneva Proteomics, MDS Proteomics, Oxford Glycosciences, and PepMetric Technologies, which had popped up hoping to capitalize on the promise of proteomics, went out of business.
Meantime, firms that have weathered the downturn such as the NextGen Group and Kinaxo Biotechnologies have stayed around by relying in large part on outsourced work from large pharmas after they shut down their internal proteomics divisions.
NEPAF, too, will depend on large pharma as a revenue generator, but it will also pursue drug makers who may not have multi-million dollar capital budgets.
“What we found are two kinds of baselines from that [market],” Kemp said. “One is spin-out companies who simply do not have the capital to invest in that kind of technology, often coming from a university background.
“The other is medium-sized pharmaceutical companies and medium-sized companies such as immuno-diagnostic type companies where we are able to provide them an extra analytical tool so that it helps them understand their own products better, it helps them characterize and troubleshoot and identify issues with their products,” he added.
NEPAF has been working with regional pharma and academic research groups, and with the official launch is now looking to expand its reach internationally, Kemp added.
Even if the proteomics service landscape has thinned out in recent years, the field doesn’t lack for players that provide proteomics analyses for a fee, if contract research organizations and core facilities are included in the mix. One way NEPAF is trying to separate itself from rivals is by taking a more collaborative approach with its clients, according to Kemp.
Proteomics service companies, he said, traditionally have been guns for hire: A client gives them some samples, tells the proteomics firm what needs to be done, then goes away. After the service company generates the data, it gives them to the client, and the project is essentially over.
But NEPAF doesn’t “just take in the sample [and] churn out the data. …We arrange everything from very small, simple samples if it’s a pure protein ID for single proteins, to much larger-scale biomarker-discovery projects. We cover a much wider range” of services, he said, including designing and redesigning experiments.
It may also involve telling a client his project may not be of any use.
“If ultimately we felt that they were wasting their money, we would tell them that this would not be the way they should be spending their money,” Kemp said. NEPAF would suggest alternative methods or do a smaller scale study to determine the utility of a project, and afterward, “if we truly felt that the project was not rigorous, was not scientific, [and] the data was quite frankly not worth the money, I think, in all conscience, we would have to decline that.”
NEPAF currently employs six scientists, led by Achim Treumann, formerly the director of the proteomics and mass-spectrometry facility at the Royal College of Surgeons in Dublin, Ireland. The facility is outfitted with five mass specs: a Bruker HCT Ultra LC-ETD/ESI MS; a Bruker Ultraflex II MALDI TOF/TOF; an Applied Biosystems/Sciex 4800 MALDI TOF/TOF/; an ABI/Sciex 4000 QTrap; and a Thermo Fisher Scientific Orbitrap LTQ LC/MS with electron transfer dissociation.
The facility is also looking to purchase a triple-quadrupole instrument. The only major mass-spec platform it will not run is an ion trap — the workhorse instrument among mass specs. This is because one of the considerations in deciding what instruments to buy was to make sure NEPAF would not duplicate what is already available in the area, Kemp said, and other facilities and institutions nearby already have ion traps.
In outfitting NEPAF with the different platforms, “the consideration was really to give us flexibility,” Kemp said. “Rather than to have one set of the same thing, the idea is each of these things have its own specialized capabilities.
“It may be that in the future as we develop and as we grow we see a particular theme or stream of activities more than others and that will help dictate what the next kind of equipment we buy and what else we might want to double up with,” he said.