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Sciex Moves to Develop Protein Quant Content With Fred Hutch-CPTAC Immuno-MRM Deal

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NEW YORK (GenomeWeb) – With the collaboration announced last month between Sciex and Fred Hutchinson Cancer Research Center researcher Amanda Paulovich, the mass spec vendor is taking on a more active role in generating protein assay content for its instrument systems.

Under the agreement, Sciex obtained the rights to commercialize immuno-MRM assays developed by the Paulovich lab through its work as part of the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium.

Sciex plans to offer the immuno-MRM assays as kits covering sample prep and protein digestion as well as immuno-enrichment of specific peptide targets. According to the company, the kits will be validated for use on a fully automated targeted proteomics system that will include the Beckman Biomek Laboratory Automated Workstation (owned by Sciex parent firm Danaher) as well as Sciex's microflow LC and QTRAP 6500+ mass spec.

The agreement is somewhat novel in the world of targeted proteomics in that, while major mass spec vendors have long pushed their instruments for peptide quantitation and, in some cases, have inked marketing agreements with protein quantitation firms to provide such assays on their systems, they typically haven't themselves offered much in the way of protein quantitation kits.

The hope is that by offering such kits, Sciex will help drive use of immuno-MRM techniques, Aaron Hudson, the company's senior director of academic and clinical research business, told GenomeWeb. While researchers are interested in the technique, he noted, the lack of off-the-shelf content has slowed its adoption, he said.

"The ability to combine the sensitivity of antibodies with the specificity of mass spectrometry has been around for a little while ... and our analysis really suggests that the reason this has not taken off more is the lack of content," he said. "People look at it and say, 'Yeah, it makes a lot of sense, where do I buy the kit?' And there just really aren't many [vendors] at the moment."

The primary commercial vendor for immuno-MRM kits and reagents currently is SISCAPA Assay Technologies, which was founded in 2011 by CEO Leigh Anderson to commercialize the SISCAPA immuno-MRM technology he invented.

Short for stable isotope standards and capture by anti-peptide antibodies, SISCAPA uses antibodies to pull down target peptides prior to MRM mass spec analysis. This helps to increase the sensitivity of mass spec instruments, which by themselves are often not sensitive enough to detect low-abundance proteins in complex samples. Additionally, by providing the mass spec with a cleaner sample enriched for the targets of interest, SISCAPA can reduce LC and instrument cycle times, upping assay throughput.

Mass spec is an attractive alternative to immunoassays for protein quantitation both in research and clinical settings because its multiplexing capabilities make it potentially less expensive, and mass spec assays often have better specificity than immunoassays, providing a higher level of confidence that the analyte measured is, in fact, the assay target.

Indeed, Hudson said, due to the limitations of immunoassays and issues with antibody quality more generally, "there is really a groundswell, I think, to try to have an alternative technology that can do [protein quantitation] better, and for us I think that is immuno-MRM."

However, as he noted, limited access to immuno-MRM assay kits has hindered uptake of the methods. "The content researchers want just isn't available right now," he said.

SAT's website lists available reagents to 46 different targets, though the company also develops custom assays.

Sciex did not say how many of Paulovich's immuno-MRM assays it planned to develop into commercial kits, butHudsonsaid the company planned to begin next year offering sets of assays aimed at specific biological pathways beginning with the DNA damage pathway, which is an area of focus for Paulovich's research.

Her lab this year published a paper in Molecular & Cellular Proteomics on a 69-plex immuno-MRM assay targeting the DNA-damage response network.

Paulovich is also working in collaboration with Steven Carr of the Broad Institute and John Koomen at the Moffitt Cancer Center to develop MRM and immuno-MRM assays to roughly 100 proteins involved in RAS signaling under a contract from CPTAC. Hudson did not say if Sciex would seek to commercialize these assays, as well.

He did note, however, that this agreement was one the company planned to build on going forward and that it would possibly look into other options for adding protein quant content in the future.

Using the automated protein quant workflow Sciex has put together for use with the kits, researchers will be able to process roughly 150 samples a day when doing singleplex assays or around 50 samples a day when doing multiplex protein assays covering in the range of 20 analytes.

While the Sciex kits can, in theory, be used on another vendor's instrumentation, they will be validated specifically for the Sciex workflow, Hudson said.

"Customers can use it on another mass spectrometer, but it won't be validated on that," he said. "The idea is we are providing a validated solution so you can rely on the information. You can know that if you use the same methods and same kit in two different places on two different days you are going to get the same result. That is what we are aiming for here."

As the vendor with the largest existing triple quad installed base, Sciex has an obvious motive for driving forward MRM-based protein quant. Hudson noted that the company hopes, as well, that providing easy, off-the-shelf immuno-MRM content will bring new users to the fold.

"If there is a solution that is off-the-shelf, then that is going to influence people to buy our mass spectrometers," he said, adding that he believes "there is whole population out there" of researchers frustrated with the limitations of immunoassays who would be interested in giving mass spec-based protein quant a try were it more straightforward.

"If we can make it even simpler and kit it and bring the price down a little bit, then [mass specs] are protein analyzers essentially, and a protein analyzer that has a great deal of content where you can click on the web [for an assay kit] and get it the next day is a great path forward to advance the field," he said.

While no other vendors have yet taken the step of developing a significant catalog of immuno-MRM assays for use on their machines, some have entered agreements with other firms to push use of their instruments for such methods.

Agilent, for instance, has been particularly active, working with SAT and Anderson on fully automated immuno-MRM workflows incorporating its Bravo Liquid Handling Robot and LC-MS instrumentation. SAT is a value-added reseller for Agilent, which allows the company to help its clients set up Agilent-based systems for its SISCAPA assays.

Anderson, whose company stands to benefit from increased adoption of immuno-MRM methods, told GenomeWeb that he saw the Sciex deal as "a very positive step forward for research on signaling pathways and for SISCAPA assays in general."

He noted that "by integrating instrument platforms with assay kits, [the deal] moves the industry one step closer to the 'integrated instrument plus consumables' business model of clinical diagnostics."

"This has been challenging in the past since the sales cycles and supply chains for instruments and consumables are very different," he added.

Regarding potential clinical ambitions, Hudson noted the challenges involved in getting any test — let alone a mass spec-based protein test — through the US Food and Drug Administration.

However, he said, while the assays covered under the recent agreement are for research use only, "clearly, the biomarker discoveries of today are going to be the personalized medicine of the future and ... we believe that this type of technology is going to be important to move medical research forward."

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