How Proteomics Startups Are Overcoming Scale and Precision Challenges

The human proteome is complex, dynamic, and—until recently—difficult to map with clinical precision.

While genomics provided the blueprint for biology, proteomics offers the real-time status of human health. Yet, the field has been hampered by a recurring trade-off: researchers often must choose between high-resolution molecular data and high-throughput.

To understand how the industry is moving past these bottlenecks, Technology Networks spoke with five industry experts from proteomics startups who are reimagining the proteomics workflow, and asked them the same question: “Can you tell me about your technology, and the proteomics workflow challenges that you are hoping to overcome?”

Henrik Everberg, PhD, CEO of ProteomEdge

“From my perspective, one of the most important steps forward in proteomics is moving through untargeted biomarker discovery toward targeted absolute quantification of clinically relevant disease-specific proteins, particularly in complex samples like plasma. Being able to measure proteins in a way that is directly comparable across samples and studies changes how confidently we can interpret the data.

“A lot of the work we’re doing at ProteomEdge is centered around enabling this at a larger scale. With our qRePS™ approach, we’ve developed what I would consider a very extensive panel of heavy-labelled protein standards, and with the recent DiscoveryEdge600 release, we’re now covering more than 600 protein targets in plasma.

“For me, what’s exciting is not just the number of proteins, but the ability to combine that level of coverage with quantitative consistency, preparing for validation and translation of the assay into the clinics.

“Another aspect I find particularly important is that ProteomEdge qRePS standards are introduced at the initial step of the workflow. Because they’re pre-aliquoted, dried, and provided in a 96-well plate format, they can be included right at the first step of sample preparation.

“In practice, that helps reduce variation from sample handling and creates a more controlled starting point. That, in turn, supports more reliable normalization and makes standardization and quality control much more effective throughout the process.

“I tend to think of this as bringing together two things that haven’t always gone hand in hand in proteomics, namely broad, discovery-oriented profiling and the level of control you need for confident quantification. If we can do both at the same time, and do it reproducibly across many samples, that’s where the real impact will be, especially in larger studies.

“For me, the main contribution is not just increasing scale but doing so in a way that maintains consistency and makes the data more comparable and usable over time.”

David Kotol, PhD, R&D manager at ProteomEdge

“One of our missions is to make standardization practical and to turn quantitative proteomics into something actionable.

“It is not only about measuring more proteins. It is about generating data that supports biological interpretation, allows comparison across studies, and helps guide clinical decisions.

“By integrating qRePS early in the workflow with ready-to-use panels, we reduce uncertainty and move closer to proteomics that is scalable, reproducible, and ready for real-world application.”

Andrew Heron, PhD, CEO of Portal Biotech

“Workflows today either sacrifice molecular resolution for accessibility or rely on expensive, low-throughput, highly specialized mass spectrometry that still fragments the underlying molecular information.

“Portal Biotech is bringing next-generation sequencing to proteins, delivering accessible, benchtop nanopore systems that read full-length molecules directly, at single-molecule resolution, in real-time. No fragmentation, no reconstruction, just intact proteins, capturing biology as it actually exists.

“This fundamentally changes where and how proteomics is done, moving from centralized, service-based workflows to high-throughput, rapid characterization at the point of need, including directly where biologics are developed and manufactured, while delivering class-leading molecular information.

“This is the same inflection point that genomics experienced a decade ago. 

“Once proteins can be sequenced directly and at scale, biology becomes computable, unlocking predictive insight that will transform drug discovery and diagnostics.”

Amos Chungwon Lee, PhD, CEO and co-founder of Meteor Biotech

“The modern spatial proteomics workflow faces two major bottlenecks: sample degradation and target limitation.

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“Traditional physical extraction methods, like UV-based laser capture microdissection, cause thermal damage that degrades proteins and post-translational modifications. Conversely, in situ imaging mass spectrometry platforms (such as Hyperion) require extensive antibody labeling. This targeted approach restricts researchers to a predefined panel of proteins, meaning any novel or unlabeled proteins in the tissue are completely missed.

“Meteor Biotech was founded to overcome both of these limitations. We developed CosmoSort, a spatial omics platform powered by our proprietary SLACS (Spatially-resolved Laser-Activated Cell Sorting) technology.

“CosmoSort utilizes a highly precise, low-energy infrared laser to physically extract specific regions of interest down to the sub-cellular level with minimal damage. Because we safely extract the intact biological material rather than just imaging a tagged panel, our platform does not require targeted labeling.

“We seamlessly bridge high-resolution spatial mapping with downstream, unbiased liquid chromatography-mass spectrometry.

“This empowers translational researchers to perform truly label-free discovery, capturing the entire spatial proteome—including unknown and unlabeled proteins—with pristine fidelity directly from the tumor microenvironment.”

Robert Moritz, PhD, co-founder of Axoiya

“Our novel SuperBinder technology has a higher affinity and streamlined approach for the enrichment of phosphotyrosine-containing peptides for proteomics analysis.

“We see up to 10x more recovery of tyrosine phosphorylated peptides than traditional immobilized metal affinity chromatography methods. In addition, our optimized AxoBind enrichment kits include all buffers and sample cleanup plasticware in addition to our novel SuperBinder beads to enable ease of use, automatable phosphopeptide enrichment, and a simple-to-follow standardized protocol, which enables high reproducibility between samples.

“AxoBind-pY SuperBinder is the first product we brought to market, and we have many other SuperBinders under development to be released this year, including methylation, phosphohistidine, neddylation, and others. Our standardized enrichment kits aim to overcome the lack of comparison and sample-to-sample reproducibility perennial amongst post-translational proteomics approaches due to the researchers having to develop their own methods and approaches duplicated across laboratories worldwide.”