How Industry Is Moving Proteomics From Discovery to the Clinic

Proteomics is no longer judged solely by the depth of discovery it enables, but by how effectively those discoveries can be carried into clinical research, drug development, and patient care.

As technologies mature and datasets grow larger and more complex, the field faces new challenges: reproducibility, standardization, quantitation, and workflow scalability. Meeting these demands is essential if proteomics is to move beyond the research lab and become a routine tool in applied and clinical settings.

To explore this, Technology Networks asked a group of industry leaders a common question: “How is your organization contributing to the shift from translating proteomics research into clinical and applied settings?”

Their responses highlight the strategies being pursued across the proteomics ecosystem, from platform design and assay development to sample preparation, data workflows, and clinical-grade validation.

Jenny Samskog, PhD, head of product management, Olink Proteomics, part of Thermo Fisher Scientific.

We continue to focus on achieving an in-depth understanding of the proteome, both through increasing our assay library to optimally represent the human proteome and by supporting the research community in integrating large, multi-dimensional datasets. This includes enriching proteomic data with insights from other technologies and linking it to large population cohorts such as the UK Biobank.

To advance discoveries from the research lab to the clinic, it’s essential to have a detailed understanding of assay performance and strong absolute quantitation capabilities—both key areas of investment for us.

Katherine Tran, senior global market development and marketing manager, Proteomics, SCIEX.

We launched the ZenoTOF 8600 system this year, which highly aligns with the goal of shifting proteomics from a translational approach to a clinical and applied setting.

The ZenoTOF 8600 system combines the triple quadrupole front-end ion guide and ion source that SCIEX is known for, with an enhanced Zeno trap-enabled QTOF, featuring a new optical detector, to offer an ultra-sensitive, accurate mass spectrometry solution. It opens up the ability to perform discovery-level research and targeted proteomics all on one system.

Previously, this would have been done on two different systems: discovery on an accurate mass system and targeted verification on a triple quadrupole. By completing the workflow on one system, we aim to deliver reduced operational complexity, reduced footprint, and maximized energy efficiency.

Henrik Everberg, PhD, chief executive officer, ProteomEdge.

ProteomEdge was founded to support the full translational proteomics workflow, from biomarker discovery to application-specific measurement.

On the discovery side, panels such as DiscoveryEdge175 and the soon-to-be-launched DiscoveryEdge600 enable broad, hypothesis-generating protein profiling to identify promising biomarker candidates for further analysis.

On the application-specific side, ProteomEdge develops panels with selected, relevant targets such as ApoEdge, LiverEdge, ThromboEdge, and ComplemEdge. Using heavy-labeled quantitative recombinant protein standards, generating multiple peptides per protein, in vacuum-dried and plate-based formats that support high throughput and reproducibility. These panels can easily be customized to specific diseases, pathways, or clinical questions.

As targeted proteomics scales, data processing, quality control, analysis, and interpretation become major bottlenecks. ProteomEdge therefore combines assay development with structured data workflows and LIMS-compatible processes, ensuring that both samples and data can be handled reliably at scale.

Sameer Vasantgadkar, senior manager, Omics Solutions at Covaris.

Covariance is a sample prep company. We offer focus ultrasonicators that can be used heavily in different ways for all kinds of omics applications. Essentially, it is a standard platform that you can use for processing different kinds of sample types, such as blood, formalin-fixed paraffin-embedded tissue, saliva, fresh/frozen tissue, plasma, etc., in a format that is compatible with the user's needs.

You have solutions that you can do in a single sample, 8-well, or 96-well, which gives you the flexibility and the scalability to future-proof your workflows, as well as a technology that is compatible with different workflows—it could be liquid chromatography-mass spectrometry, or ELISA-based workflows. You have one single solution, which gives you a really high-quality readout for your sample prep.

Stephen Williams, PhD, chief scientific officer, Alamar Biosciences.

Dr. Williams previously served as chief medical officer at Standard Biotools (post-merger with SomaLogic) at the time of the discussion.

The core of our contribution is the SomaScan assay that currently measures 11,000 proteins. When thinking about the shift into translation, from discovery into the clinic, we have 17 multivariate tests that have done that translation.

We use machine learning and large-scale studies to identify the patterns, the mathematical equations, and then we've validated those in multiple data sets and taken them through to the clinic. For example, the 27-protein model has been used in ~60,000 people in 24 clinical trials, to predict the absolute likelihood of having a cardiovascular event or dying, and it's used all the way through to healthcare. Along with that, we've got liver, kidney, dementia prediction, body composition tests, and so on.

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We've made that transition to the clinic because of the long-term calibration and consistency of the assay platform. But at the moment, the biggest users are a combination of roughly 50% in pharma, using the assay in clinical trials, which include one or more of these tests, and some of those users are using it for proof of drug mechanisms, so individual proteins.

For the tests that have been applied to healthcare, their predominant use today is in clinical trials, to find unexpected benefits or adverse effects of drugs, as well as individual proteins.

Yuling Luo, chief executive officer and founder, Alamar Biosciences.

The robustness and consistency of the assay and technology have become critically important because you need to have that precision, consistency, and the simplified workflow to convert whatever you discover into translation and diagnostics. Very few discovery platforms have the capability, or it was built for translation and diagnostics, and this is where Alamar has a unique advantage.

The platform was intentionally built for translation and diagnostics; we are ISO 1345 compliant for manufacturing the reagents and the reagent kits. From the very beginning of this company, our mission has been to power precision proteomics to enable the earliest detection of disease.

That's why we need to create long shelf-life reagent kits, which take a lot of work and come in dry powder form instead of liquid. It's not easy, because you have to lyophilize the antibody and antigen, and you have to lyophilize your controls. You have to lyophilize the enzyme polymerase, the ligase, and then ensure its functionally stable.

We spent five years developing the platform before we commercialized; all the pieces have to be put together, but we do this hard work so our customers will have an easy experience. Our customers can have this push-button solution that can ensure consistency, robustness, and ensure there's less user error, just because the workflow is so simple.

I think that's the difference between a pure discovery platform that is enabled by other technologies vs our discovery platform. Whatever our customers discover with our platform, they have a seamless path towards translation and diagnostics all in one, and we are the only platform that's all in one that covers the entire journey from discovery to translation to diagnostics. No other discovery platform was built for that, and we will purposely build this clinical-grade platform with the capability for discovery.