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Sciex Increases Throughput of Proteomics Workflows While Eyeing Clinical Applications

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NEW YORK (GenomeWeb) – With the opening this year of the University of Manchester's Stoller Biomarker Discovery Centre in the UK and the Australian Cancer Research Foundation International Centre for the Proteome of Cancer (ProCan) in Sydney, mass spec vendor Sciex has made significant strides in the implementation of what it has dubbed "industrialized proteomics."

Based on the company's Swath data-independent acquisition workflow, this approach to proteomics research is marked by a shift in focus from maximizing proteome coverage toward establishing robust systems enabling reproducible, highly automated workflows capable of profiling tens of thousands of samples.

The company is at the same time working on methods to move protein biomarkers and other discoveries made through such research into the clinic, and views targeted mass spec as a technology well suited to translating findings from large-scale precision medicine initiatives, Sciex President Jean-Paul Mangeolle told GenomeWeb this week.

Proteomics has in recent years made significant advances in throughput. For instance, five years ago, SISCAPA Assay Technologies CEO Leigh Anderson lamented in a presentation at the Association for Mass Spectrometry: Applications to the Clinical Lab's annual meeting that of the thousands of biomarker proteomics papers published, he didn't know "of a single one in which anybody has actually run 1,000 samples."

Since then, advances in mass spec instrumentation and workflow automation have made experiments looking at thousands of samples entirely feasible, if not yet routine. ProCan, for instance, plans to profile roughly 70,000 cancer tumor specimens over the next seven years, while the Stoller Centre likewise aims to run on the order of thousands of samples.

Sciex, specifically, has "put a significant amount of energy over the last few years working on key points in the proteomics pipeline to try and industrialize the overall workflow," Mangeolle said. He cited as essential parts of the company's approach the automation of protein digestion; the use of microflow liquid chromatography, which offers improved robustness compared to nanoflow; the use of cloud computing (via Sciex's OneOmics collaboration with Illumina) for data processing; and the use of its Swath DIA mass spec technique.

This last component is perhaps the key to Sciex's "industrialized proteomics" aims. As Stoller Centre Director Tony Whetton told GenomeWeb last year, Swath-style mass spec is well suited to large-scale biomarker work due to the relative ease and speed of the method.

He compared it to the isobaric tagging methods his lab used previously and which remain a popular tool for quantitative proteomics studies.

"Isobaric tagging is a very great deal slower, so if you want to crank through a great many samples, then it is extremely difficult," he said. "The Swath MS technique is going to give you just as good a penetration at probably 10 percent of the machine time. I think also the informatics [in isobaric tagging] is a bit more challenging."

Additionally, because Swath-style data-independent acquisition (DIA) mass spec methods collect MS/MS spectra on all ions in a sample, the technique avoids the issue of stochastic sampling that exists with traditional shotgun approaches. This means that while DIA methods don't typically identify as many peptides in a given sample as shotgun methods, they provide more reproducible quantitative information on the peptides they do identify, which makes the approach well suited to quantitation of large sets of proteins across large numbers of samples — as is required in biomarker discovery and validation.

Mass spec is well established as a biomarker discovery tool, whether via Swath and related DIA techniques or conventional data-dependent methods. Its utility as a clinical platform for measuring the biomarkers identified in such discovery experiments remains less clear. Researchers and clinicians have put considerable effort into developing targeted mass spec assays for clinical use, but with limited success to date.

Mass spec's complexity and long (at least compared to common immunoassays) turnaround time continue to make it a difficult sell as a clinical technology. It has managed to gain a foothold for certain assays, like thyroglobulin testing, where existing immunoassays had obvious flaws, but, such examples aside, it has made little headway as a replacement for conventional tests.

And while companies including Integrated Diagnostics and Sera Prognostics have released new proteomic tests on mass spec platforms, the majority of such tests still comes to market in immunoassay format.

Mangeolle said, however, that he believed mass spec would continue to carve out a role as a clinical platform. He cited the company's formation in 2014 of its Sciex Diagnostics division, which offers regulatory compliant medical device versions of its triple quadrupole and QTRAP instruments. Sciex also sells mass spec-based in vitro diagnostic kits in Europe for newborn screening, immunosuppressant testing, and vitamin D testing.

He said Sciex planned to focus its attention on assays where conventional immunoassays are poorly suited — in cases where antibody specificity or multiplexing needs present challenges, for instance.

He added that for biomarkers discovered using mass spec platforms, there may be an advantage in terms of assay development to sticking with mass spec for translation to the clinic. In this he echoed comments from Integrated Diagnostics CEO Albert Luderer, who told GenomeWeb in an interview last year that moving from the company's mass spec discovery platform to an antibody-based clinical assay for its Xpresys lung cancer test would have added an additional two years to its commercialization process.

"It is very hard to actually execute a technical strategy [in proteomics] without using mass spec, and we think that proteins are where the action is going to be," he said at the time. "So, I think if there is going to be a future for new analyte discovery in the proteome, mass spec is going to be a central player."

Luderer also noted, however, that if, as Indi gathers more information on the Xpresys test, it is able to winnow down the test's panel of proteins, it would consider transitioning to an immunoassay format.

"The time to get an answer is going to be a lot shorter because the analytic preparative steps for an immunoassay are just much simpler than they are for a mass spec," he said. "Time is money, and turnaround time also [affects] the expectations of physicians ordering the test."

“Clinical chemistry labs are really driven by improving patient care and keeping the cost of testing down," Mangeolle said with regards toSciex's vision of mass spec's potential role in the clinic. "Immunoassays are fast, cheap, and automated, and in nearly all cases for current assays, are good enough to make the right diagnosis. LC/MS still has to get a lot simpler, more robust, and have greater throughput if it’s going to be adopted into mainstream testing."