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Automation, Microsampling Key to Clinical Adoption of Mass Spec-Based Proteomics, Researcher Says


Jennifer Van Eyk, director of the Advanced Clinical Biosystems Institute at Cedars Sinai Medical Center, has for years been a leading researcher in proteomics and mass spectrometry, applying these tools primarily to the study of the molecular basis of cardiovascular disease.

In a recent commentary in Clinical Chemistry, Van Eyk put forth the case for clinical proteomics, and mass spectrometry-based clinical proteomics in particular, highlighting the field's ability to provide both better-performing biomarkers and improved methods for measuring them. 

The advantages that Van Eyk and her co-author and Cedars Sinai colleague Ian Wright cited for mass spec-based clinical proteomics, such as the ability to better measure protein variants or post-translationally modified proteins and the potential for remote, longitudinal patient testing, are relatively well-trod territory. However, speaking to GenomeWeb this week, Van Eyk said that developments over the last year suggest that these benefits — which to date have largely remained theoretical, at least so far as clinical assays are concerned — are on the cusp of being realized.

Two factors, in particular, have contributed to her optimism regarding the near-term future of mass spec-based clinical proteomics, Van Eyk noted — the emergence of microsampling devices suitable for in-home blood collection, and her lab's ability to develop highly automated and reproducible workflows for both targeted quantitation and discovery of and biomarkers using these microsamples.

The developments, she said, indicate that mass spec could become the tool of choice for applications like large-scale epidemiological studies and long-term monitoring of at-risk patients or patients with chronic diseases, potentially giving the technology the foothold it needs to carve out a significant space in the clinical market.

Until recently, the primary challenges of mass spec-based proteomics in terms of moving into the clinic were largely technical. The technology and its proponents needed to demonstrate that it had the throughput, accuracy, and reproducibility required for running clinical assays.

Those challenges have largely been overcome. While development of clinical proteomic assays is far from trivial and optimization remains to be done, particularly with regard to standardizing assays across different laboratory sites, companies like Integrated Diagnostics and Sera Prognostics have released commercial multiplexed proteomic tests on mass spec platforms and a number of other clinical firms have started using mass spec for applications like thyroglobulin testing where existing immunoassays were significantly flawed.

Today, perhaps the most significant challenge for mass spec-based clinical proteomics comes from the business side.

"I have always said that the thing we are missing is what [application] is going to drive this whole movement of mass spectrometry into the clinic," Van Eyk said. "It has to be something compelling that would make a good business model."

"I think that some of these microsampling devices, coupled with automation, might be what it takes," she added.

The notion of mass spec as a tool for enabling in-home sampling has gathered momentum in recent years as interest in in-home blood sampling has grown more generally. Much of this has revolved around the use of dried blood spots, which are a well-established sample source for newborn screening and are growing in popularity for drug development and clinical trial work.

Because dried blood spots involve a simple finger prick as opposed to a blood draw and can be sent unrefrigerated through standard mail, they offer significant advantages in terms of convenience and cost. And, were the clinical testing industry to move toward dried blood spots as a sample source, mass spec could prove an effective technology for running such assays.

As SISCAPA Assay Technologies Founder and CEO Leigh Anderson told GenomeWeb in an interview earlier this year, "As long as we are drawing big tubes of blood, there is plenty of sample to do as many immunoassays as you need," Anderson said. "But in a world of microsamples like dried blood spots, there isn't enough material to divide between all the immunoassays you might want to run. So with that kind of sample, you need to be able to multiplex your tests on a very small volume."

Anderson, who is currently exploring clinical proteomic applications of dried blood spots, further noted that the approach offers the potential for "enormous improvement in patient convenience and a really profound cost improvement compared to people having to go to a clinic or a doctor's office and get blood drawn by a phlebotomist and [the clinic] then [having to] ship those samples cold by FedEx."

Van Eyk suggested a similar vision, but instead of dried blood spots, her lab is using a device from microsampling firm Neoteryx that is capable of drawing a specific volume of blood, 10 microliters in the case of her own work. Though Anderson and other researchers have done work on standardizing proteomic measurements in dried blood spots, the ability to do volumetric microsampling is, to her mind, a key advantage of such systems over dried blood spots, she said.

"There are lots of good things about dried blood spots, but there are things that make it challenging," Van Eyk said. "I have dabbled a little in dried blood spots, but I just don't like things that can't be QCed, and that are dependent on lots of different factors. I don't know how you do it when you don't have a volumetric draw. So I was very interested in the Neoteryx product."

She and her colleagues have developed an automated mass spec workflow, in collaboration with Beckman Coulter and Sciex, that handles sample prep including protein denaturation, reduction, alkylation, and digestion through to mass spec analysis. Using this system to analyze samples collected using the Neoteryx device, they have built 10-plex and 73-plex targeted proteomics assays and a Swath data-independent acquisition assay that can reproducibly quantify more than 500 proteins for discovery experiments. All of the measurements in the two targeted assays have coefficients of variation of less than 20 percent, while for the Swath assay, 350 of the 500 or so proteins are measured with CVs below 20 percent.

This, Van Eyk said, indicates the feasibility of using mass spec, combined with at-home microsampling, for regular patient monitoring, a possibility that she, like Anderson, noted could drive clinical uptake of the technology.

"Can you imagine if everyone who has had an operation at Cedars Sinai Medical Center is released and we are able to monitor them over time at home?" she said. "Can you imagine if you are living in the middle of nowhere and you can have your heart [condition] monitored by sending in your blood samples to us without having to go and see your local doctor, who may be miles and miles and miles away?"

"There are lots of issues with Theranos," she said, "But for some of it, they got the business plan right. This [sort of remote monitoring] is what people have been talking about with things like dried blood spots, but it's not trivial to do. So now if we can make that trivial, if we can reduce those barriers, then I think that is another driver [for clinical mass spec]."

The other half of the equation is discovering and validating new markers for which mass spec is particular well suited, Van Eyk said. Here, too, the combination of microsampling and high-throughput, highly reproducible workflows will help yield results, she suggested.

"I have always said that post-translational modifications or genetic variants are going to give us that fine tuning we need for [effective] biomarkers and that they would also be driving forces to get [mass spec] into regular clinical chemistry labs," Van Eyk said, noting that she has begun to see more such markers making their way toward clinical practice.

She cited as an example apolipoprotein L1, where certain variants have been shown to be relevant to identifying patients at risk of cardiovascular and chronic kidney disease. Another example, she said, is b-type natriuretic peptide (BNP), which is one of the primary markers for heart failure.

Recent work, including by Van Eyk and her colleagues, has shown that BNP is proteolyzed quickly in the blood, raising the question of how effective existing immunoassays are at measuring this analyte.

Mass spec, on the other hand, "certainly has the ability to monitor [BNP] degradation and find out whether it is active or not active," she said, adding that she has begun to see more and more biomarker assays that take into account protein variants or degradation patterns. "And mass spectrometry I think is going to be the best way to measure that kind of biology."

Also key, Van Eyk said, is involving epidemiologists and population scientists with access to, and experience with, the large cohorts required to demonstrate the clinical utility of new markers and new modes of testing, like regular in-home monitoring.

To that end, her lab has received funding through the National Heart, Lung, and Blood Institute's Trans-Omics for Precision Medicine (TOPMed) program that will allow it to access large clinical cohorts for proteomics research.

"You have to have that academic epidemiology population science along with high throughput and good assays to really get the validation that is required," she said. "And I can see that all happening now, really, over the last six months to a year."