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BGI Aims to Expand Proteomics Services, Purchase 50-Plus New Mass Spectrometers

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By Adam Bonislawski

This article was originally posted on June 14.

Known primarily for its genomics work, Shenzhen, China-based research institute BGI is looking to expand its proteomics offerings and plans to buy roughly 50 new mass spectrometers over the next two years.

The sequencing powerhouse — it currently runs more than 160 next-generation sequencers from Illumina and Life Technologies — aims to purchase around 15 new high-resolution mass specs and between 30 and 40 triple quadrupoles machines, which it will distribute among its six Chinese research facilities, Siqi Liu, associate director and head of BGI's proteomics division, told ProteoMonitor.

In 2010, Liu said, BGIs proteomics division generated approximately ¥40 million ($6.2 million) in revenues, primarily from the sale of technical services to researchers and pharmaceutical firms. Moving forward, he said, BGI hopes to expand beyond the services business and into more clinical and drug-development applications.

"Currently we're offering mostly [proteomics] technology services," Liu said. "We have the machines and the experience and especially we have good teams in bioinformatics, so we do a lot of project [work] in China. But we can't stay at this stage. We really want to [develop] mass spec techniques to where they can go into the [clinic]. We want to be able to run protein biomarker [assays] with high throughput and high sensitivity on mass spec."

"Another thing we would like to provide are drug screening services," he added. "There are a lot of [pharma] companies that need [proteomics] assays, so if we can provide them accurately on a large scale, [drugmakers] would like that very much."

He cited phosphoproteomics screening for changes in kinase activity in response to drug treatment as one such potential application, noting that drug companies are interested in "looking [at kinase activity] globally after drug use. It's quantitative phosphorylation, so you can see the time dependence [and]?the dose dependence."

BGI is currently developing such assays, Liu said, "but they aren't yet as the stage where we can make them available as a service."

"Proteomics is technically still a very tough, very immature” technology, he said, noting that the organization has devoted a significant amount of its proteomics resources inward, "working in R&D, on just the technical side" because "we can't offer services if our technology is not mature and the reproducibility isn't good and our CVs are too large."

Currently, BGI's proteomics offerings are good enough technically to make it "probably the top in China," Liu said, "but I don't think technically we are very good compared to [proteomics firms in] the United States." The proposed scale of BGI's mass spec operations, however, should make it the largest proteomics services provider in any country.

Chinese firms are in general relatively weak players in proteomics, said Jim Zhang, principal of JZMed, a Rensselaer, NY-based consulting firm offering services to western biotech companies looking to outsource work to China.

"Proteomics in China is relatively new and weak at this moment," he told ProteoMonitor, adding that a recent report prepared by JZMed counted only nine companies in the country currently providing services in the space.

China is the primary market for BGI's proteomics services at present, but it hopes to expand its business in the US, Liu said, particularly given that the US “probably has a bigger market than in China for pharmaceutical work."

Last year, BGI set up two affiliates — BGI Americas and BGI Europe — to coordinate partnerships with research institutes and commercial entities in the US and Europe.

BGI has been doing work for Merck as part of a collaboration agreement the two groups signed in September of last year (GWDN 09/15/2010). That deal focused mainly on BGI's next-generation sequencing capabilities, but, Liu said, it has also involved its proteomics division, running immunoaffinity mass spec assays on protein targets specified by Merck.

"They are providing the antibodies and we're doing the [immunoprecipitation] and [multiple-reaction monitoring] mass spec," he said, adding that while BGI has done some small proteomics projects for US pharmas, this is the largest such deal the division has been a part of thus far.

In terms of clinical proteomics like protein biomarker-based diagnostics, Liu sees BGI's biggest opportunities coming in China. It is looking to get involved in the National Cancer Institute's Clinical Proteomic Technologies for Cancer initiative and will be attending the group's annual meeting this year, but, Liu said, "based on my understanding, there are a lot of [regulatory] issues" to clinical work in the US that may make China a more attractive market with regard to that space.

In China too, however, moving mass spec-based proteomics into the clinic remains a difficult task, he added. "If everyone today is using ELISAs and you say, come on, use mass spec, the Chinese [State Food and Drug Administration] may not approve it," he said. "It may take a couple of years, the same as in the [US]. You have to convince people that [mass spec] is the best way.

"We're still in the learning stage” with clinical proteomics, Liu said, noting that in addition to mass spec-based assays, BGI's proteomics division is working on antibody generation, multiplex ELISAs, and protein chips among other technologies.

In 2007 BGI's protein chip-based Array-ELISA diagnostic kit for autoimmune diseases received approval from China's SFDA. It also advertises on its website that the Array-ELISA platform can be used for research into areas including tumor markers, cytokines, and cardiovascular disease.

According to Zhang, protein chip-based diagnostics for viral diseases like HIV and HPV are also a "rapidly developing" market in China.

"We want to apply mass spec to the clinic, to biomarkers, but this is in the future," Liu said. "I can't see that in two or three years mass spec will replace ELISA, but in the future [it] at least will be one of the choices."

According to Liu, BGI currently has twelve mass spectrometers – six each in its Shenzhen and Beijing facilities – including Thermo Scientific LTQ Orbitrap Velos, Bruker maxis, and AB Sciex QTRAP 5500 instruments.

The Orbitraps have emerged as "workhorse" machines, he said, adding that with regard to the 15 high-resolution machines it plans to add, BGI is looking closely at AB Sciex's TripleTOF 5600 and Thermo Fisher's new Orbitrap Elite machine.

The plan, Liu said, is to distribute the machines throughout BGI's six Chinese branches, keeping R&D and assay development at its Shenzhen headquarters.

"We'll standardize the protocols in Shenzhen, and when the technique is mature we can just send it to the other branches and everyone will just follow that," he said. As part of this standardization process the institute plans to make its mass spec instrumentation more uniform as well, he added.

"Right now we have a lot of different machines," he said, "but later on we'll probably just select one. Say [for example] the QTRAP 5500 is working perfectly for [a particular assay]. We'll just fix on that one machine, then."


Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.

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