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New Study Further Bolsters Case for Bruker's MALDI Biotyper as Broad Clinical Proteomics Platform


Scientists from the University of Victoria, SISCAPA Assay Technologies, and Bruker have demonstrated the use of MALDI mass spectrometry for quantifying levels of the putative prostate cancer marker protein C inhibitor in clinical samples.

Significantly, the researchers measured the marker on Bruker's Microflex LT instrument, the system used in the company's MALDI Biotyper platform. Bruker has, to date, aimed that platform primarily at the clinical microbiology market, but recent collaborations – including this work with U-Vic and SAT – suggest that the company is now trying to establish the system as a tool for clinical proteomics more broadly.

Generally speaking, the field has viewed multiple-reaction monitoring mass spec on triple quadrupole instruments as the likeliest route for mass spec-based proteomics to move into clinical applications, with MALDI traditionally being dismissed due to concerns about its sensitivity and reproducibility.

Some recent studies, however, have indicated that MALDI might prove a suitable technology for clinical proteomics, where it could offer advantages in terms of throughput and ease of use. And, as interest in using MALDI for clinical proteomics grows, Bruker's Biotyper could emerge as a primary platform for these efforts.

The system's potential as a clinical proteomics platform stems largely from the fact that it is already in use in hospitals and reference labs around the world as a platform for clinical microbiology. Since launching the instrument in 2006, Bruker has placed more than 800 worldwide and has obtained clearance for clinical use of the instrument in Europe, Australia, New Zealand, Taiwan, and Japan. The company is also pursuing 510(k) clearance from the US Food & Drug Administration and expects to receive a ruling sometime late this year or in early 2014.

Given the device's large installed base and extensive clinical approvals, the Biotyper represents "a very interesting case of mass spectrometry getting into clinical use almost under the radar ... and an interesting potential avenue to introduce mass spec protein assays," SAT CEO Leigh Anderson told ProteoMonitor.

The U-Vic, SAT, Bruker collaboration on MALDI-based measurements of PCI originated from work done by Morteza Razavi, a graduate student in the lab of U-Vic researcher and SAT Co-founder Terry Pearson. Detailed in a paper published last month in Clinical Chemistry, the project initially used an AB Sciex 4800 MALDI TOF/TOF instrument to quantify the protein. The researchers then moved the assay to the lower-performance Microflex LT out of "a sort of scientific curiosity of how much [mass spec] resolution and performance would it take to make the assay work quantitatively," Anderson said.

"We did that without expecting that it was going to work well, but it worked very well," he said. Running SISCAPA MALDI assays, which use an immunoenrichment step upfront of mass spec analysis to isolate target peptides, the researchers achieved a mean coefficient of variation of 5.8 percent and a limit of quantitation of 20.2 femtamoles on the Microflex LT.

The apparent suitability of the instrument for this sort of protein biomarker assay suggests that "all of a sudden you have [nearly] 1,000 [Biotyper] platforms out there that have already been bought" and that could be used for clinical proteomics, Anderson said.

"So that is a very attractive and interesting inventory," he said, noting that "the idea that Bruker and BioMérieux [which offers a competing MALDI-based microbiology platform, the Vitek MS (PM 7/19/2013)] are in the process of getting these instruments FDA-cleared is really the first step down the road to getting something that could be a real in vitro diagnostic solution" for mass spec-based clinical proteomics.

"It's happening in some sense more quickly than people anticipated," he added.

Indeed, in the US, some hospital microbiology labs have begun using the Biotyper as their primary tool for bacterial identification even in advance of the device receiving FDA clearance (PM 5/24/2013). Such use, Anderson noted, suggests a path by which the instrument might enter the protein biomarker space, as well, moving from hospital microbiology departments to their clinical chemistry labs.

"It seems to me that if a lab is CLIA certified so that they can run laboratory-developed tests, then they could take the Biotyper and run protein assays on it," he said. "They would be responsible for doing all the validation along the lines of what you are seeing with the initial use of the Biotyper [in hospital microbiology labs]. So there is a path to do that."

In an email to ProteoMonitor, Nathan Ledeboer, medical director for the clinical microbiology and molecular diagnostics laboratories at Milwaukee's Froedtert Hospital, said that while he and his colleagues had not yet explored the Biotyper as a tool for their clinical chemistry lab, they would likely look into it in the future. The hospital plans to transition fully to mass spec for microbe identification once the Bruker and BioMérieux platforms receive FDA approval.

The U-Vic, SAT study is not the first indication that Bruker might be interested in positioning the Biotyper as a tool for clinical proteomics more broadly. In April, the company announced a collaboration with the University of Victoria-Genome British Columbia Proteomics Centre on high-throughput Biotyper-based protein assays for determining genetic hemoglobin variants and diabetes risk (PM 4/19/2013).

That work is being done in partnership with Christoph Borchers, director of the center, and will employ the iMALDI method he has developed – like SISCAPA, an immunoenrichment-based technique.

At the time of the announcement, Gary Kruppa, Bruker's vice president for business development and a co-author on the recent SAT, U-Vic Clinical Chemistry study, told ProteoMonitor that the agreement "absolutely" signaled an effort by the company to move the Biotyper into the traditional protein diagnostics market.

"The Biotyper has been a very successful product, and we're looking for ways to leverage that success to make it even more widely accepted," he said. "The first thing that is of interest is other applications in microbiology ... and then the next phase beyond that is obviously the protein diagnostic market."

Like Anderson this week, Borchers highlighted the potential advantages of the platform's wide distribution and clinical approvals.

The Biotyper "has been sold mainly for microbiology, but this machine can be used for other clinical assays as well," he said. "It is already in the clinic. It is very robust, and I think this is the way to go right now" in terms of moving mass spec-based protein assays to market.

Tests developed under that collaboration will be commercialized through University of Victoria spin-out firm MRM Proteomics, where Borchers is chief scientific officer. He told ProteoMonitor that the researchers aim to have the assays ready for market in roughly a year.

He added that his team has contracts with several large undisclosed in vitro diagnostic firms to develop MALDI-based assays for various proteins – with some of these firms requesting assays developed specifically for the Biotyper.

Regarding the PCI assay developed by Anderson and his co-authors, the plan is now to further test it in much larger clinical cohorts to evaluate its usefulness as a marker of prostate cancer recurrence, Anderson said.

In the Clinical Chemistry study, an analysis using the MALDI assay to measure PCI levels in 34 patients found that PCI concentrations in the first 18 months after radiation treatment could predict recurrence with sensitivity of 78 percent and specificity of 85 percent. This compared to sensitivity of 22 percent and specificity of 92 percent for prostate specific antigen, the current gold standard biomarker for prostate cancer.

The researchers have several hundred additional samples in hand that they plan to analyze using the MALDI assay and are in discussion with several groups about obtaining more. They have filed patents on the assay and the marker, Anderson said.

In addition to the PCI work, Anderson and SAT are also collaborating with Bruker on improving the sensitivity of MALDI protein assays.

Even as MALDI has gained ground as a potential platform for clinical proteomics, most researchers have assumed that due to sensitivity limitations it would be useful mainly for mid- to high-abundance analytes, while low-abundance proteins would remain the province of triple quadrupole instruments.

However, Anderson said, "if you look back at the MALDI literature, there are a lot of people who over the years have achieved really high sensitivity for peptide detection," suggesting that the method might prove more suitable than thought for quantifying low-abundance protein markers.

"Going forward, that is the other focus of our work with Bruker – to really optimize the sample preparation for absolute sensitivity to see if we can exploit the enormous potential sensitivity of MALDI," he said.