Single-Molecule Protein Sequencing (SMPS) Market: Global Strategic Industry Review 2026

Why the Single-Molecule Protein Sequencing Market Exists

The emergence of the SMPS market is rooted in structural limitations of traditional proteomics. Most existing proteomics workflows depend on indirect measurement methods, such as enzymatic digestion followed by mass spectrometry or multiplexed antibody panels. While these approaches are scalable and well established, they often struggle to resolve full-length proteins, rare proteoforms, and complex post-translational modifications.

Single-molecule protein sequencing technologies aim to address these gaps by enabling direct molecular interrogation rather than statistical inference. By analyzing proteins one molecule at a time, SMPS platforms offer the potential to reveal biological variation that is obscured in bulk or peptide-level measurements. This capability is increasingly relevant as drug developers, diagnostics companies, and research institutions pursue precision medicine, biologics characterization, and next-generation biomarker discovery.

As a result, the single-molecule protein sequencing market is not positioned as a replacement for proteomics as a whole, but rather as a next-generation measurement layer within the proteomics ecosystem—similar to how next-generation sequencing transformed genomics without eliminating the broader genomics market.

Commercial Reality Versus Addressable Opportunity

While the current single-molecule protein sequencing market size stands at approximately US$420 million, this figure represents only the commercially realized portion of a much larger opportunity. True protein sequencing platforms are still transitioning from proof-of-concept to scalable deployment, and widespread adoption across clinical and biopharma workflows has yet to occur.

For this reason, industry analyses often distinguish between commercial market size and addressable market potential. On an adoption basis, as single-molecule protein sequencing technologies mature and displace inference-based proteomics methods, they are projected to address a multi-billion-dollar share of the global proteomics market. Under a base-case adoption scenario, this corresponds to an addressable opportunity of approximately US$4.1 billion by the mid-2030s.

What Companies Are Doing in the Single-Molecule Protein Sequencing (SMPS) Market

The single-molecule protein sequencing market is still in a formative phase, but company activity over the past decade clearly shows a transition from academic proof-of-concepts to early commercial platforms and, increasingly, toward scalable sequencing systems. Since 2015, progress in the SMPS market has been driven by a small number of highly specialized companies, each addressing different technical bottlenecks in protein sequencing and high-resolution proteomics.

Early Foundations: Academic Proofs and Nanopore Concepts (2015–2018)

The earliest work underpinning the single-molecule protein sequencing market originated in academic laboratories, particularly around engineered nanopores and single–amino acid detection. Research groups such as the Dekker Lab at TU Delft demonstrated that individual amino acids could be distinguished electrically as proteins translocated through nanopores.

At this stage, activity was confined to conceptual feasibility, with no commercial instruments or standardized workflows. These efforts nonetheless laid the groundwork for later startup formation and venture funding, particularly in nanopore-based sequencing approaches.

Startup Formation and Early Platform Development (2019–2021)

Between 2019 and 2021, the SMPS market began shifting from academic research toward venture-backed commercialization.

• Quantum-Si emerged as one of the earliest companies to commercialize single-molecule protein sequencing concepts. Rather than targeting full-length proteins immediately, Quantum-Si focused on single-molecule peptide sequencing, using fluorescent labeling and optical detection. This pragmatic approach enabled earlier market entry while longer-read sequencing technologies continued to mature.
• Nautilus Biotechnology entered the market with a different strategy, developing a single-molecule proteomics platform based on iterative binding and imaging. Instead of reading amino-acid sequences directly, Nautilus generates high-resolution molecular fingerprints of intact proteins through repeated cycles, positioning its platform between affinity proteomics and true sequencing.

During this period, the SMPS market was characterized by heavy R&D spending, limited commercial revenue, and strong emphasis on software and signal interpretation rather than throughput.

Platform Launches and Early Commercial Momentum (2022–2024)

From 2022 onward, the SMPS market entered a more visible commercialization phase.

• In 2022, Quantum-Si launched its Platinum™ protein sequencer, marking one of the first commercially available single-molecule protein sequencing instruments. While read lengths were limited and throughput modest, the platform validated customer willingness to pay for sequencing-grade protein data rather than inferred results.
• Nautilus Biotechnology advanced its Triad™ platform, demonstrating the ability to analyze intact proteins up to approximately 100 amino acids using its iterative mapping approach. Although not sequencing in the strict sense, the platform addressed key pain points in proteoform detection and multiplexing.
• In parallel, Portal Biotech accelerated development of a nanopore-based true single-molecule protein sequencing platform, targeting full-length protein analysis. By 2024, Portal had demonstrated prototype systems positioned as enabling intact protein sequencing for drug discovery and biologics characterization, placing it firmly in the highest-value tier of the SMPS market.

This phase marked a shift from “can it work?” to “can it be productized?”, with increasing engagement from pharmaceutical research groups and leading academic centers.

Commercial Scaling and Differentiation (2025–2026)

By 2025, company strategies in the single-molecule protein sequencing market had clearly diverged based on time-to-market versus ultimate resolution.

• Quantum-Si expanded beyond sequencing into multiplexed nanobody binding assays, achieving runs with 10,000+ molecules per experiment. This broadened its addressable customer base and improved consumables pull-through, strengthening near-term commercial viability.
• Nautilus continued positioning its platform as a high-resolution proteomics alternative to mass spectrometry, emphasizing scalability, reproducibility, and integration into existing workflows rather than full amino-acid sequencing.
• Portal Biotech moved toward scaling intact protein sequencing, focusing on biologics, protein therapeutics, and drug-target characterization. The company’s roadmap targets higher read counts per chip and eventual integration into regulated workflows, aligning with longer-term adoption.

Looking ahead to 2026, Quantum-Si has publicly indicated plans to scale its Proteus™ platform, targeting >1 million reads per chip, while Portal continues to refine nanopore signal decoding for full-length proteins.

Role of Single-Molecule Affinity Proteomics Companies

While not sequencing proteins, single-molecule affinity proteomics companies have played a critical commercial role in shaping the SMPS market.

Platforms developed by companies such as Olink and SomaLogic demonstrated that pharmaceutical customers are willing to pay premium prices for single-molecule resolution proteomics data. These platforms now account for the majority of current SMPS-class revenue, anchoring the market’s approximately US$420 million commercial base.

Their success has helped de-risk the broader SMPS market by validating demand for higher-resolution protein analysis, even as true sequencing technologies continue to mature.

Key Companies in the Single-Molecule Protein Sequencing Market

The single-molecule protein sequencing market is currently shaped by a small group of specialized companies pursuing distinct technological and commercial strategies. Rather than competing directly on a single approach, these players occupy different positions along the SMPS maturity curve, ranging from affinity-based platforms with established revenue to early-stage companies developing true protein sequencing technologies.

• Olink is a leading provider of single-molecule affinity proteomics, using proximity extension assays to detect proteins at extremely low concentrations. While Olink does not perform amino-acid sequencing, its platform operates at single-molecule resolution and has achieved broad adoption in pharmaceutical and biomarker research. Olink represents the largest commercial revenue contributor within the SMPS ecosystem and has helped validate market demand for next-generation proteomics platforms.
• SomaLogic applies an aptamer-based single-molecule detection approach to large-scale protein analysis. The company’s platform enables high-throughput, multiplexed measurement of thousands of proteins simultaneously, positioning it as a complementary alternative to antibody-based methods. SomaLogic plays a significant role in establishing commercial-scale single-molecule proteomics, particularly in translational and clinical research settings.
• Quantum-Si is among the first companies to commercialize single-molecule protein sequencing instruments, initially focusing on peptide-level sequencing using optical detection. The company has progressively expanded its platform capabilities, including multiplexed nanobody-based assays, allowing it to bridge sequencing and affinity proteomics. Quantum-Si is currently in the commercial scaling phase, with growing instrument placements and consumables revenue.
• Nautilus develops a mapping-based single-molecule proteomics platform that analyzes intact proteins through iterative binding and imaging cycles. Although it does not read amino-acid sequences directly, the platform delivers high-resolution protein fingerprints and targets applications where mass spectrometry faces scalability or reproducibility challenges. Nautilus occupies a transitional position between affinity proteomics and true protein sequencing.
• Portal Biotech is focused on true single-molecule protein sequencing using nanopore-based electrical detection. The company aims to sequence intact proteins directly, including post-translational modifications, positioning its technology as a long-term alternative to inference-based proteomics. Portal remains in the early commercial and pilot deployment stage, but represents one of the highest-value innovation trajectories within the SMPS market.
• Encodia is developing a fluorescence-based protein sequencing platform, leveraging cyclic labeling and imaging strategies. The company’s approach targets scalable sequencing chemistry while managing signal complexity through computational decoding. Encodia remains in the development phase, with commercialization expected as throughput and accuracy thresholds improve.

Together, these companies illustrate a layered competitive structure in the SMPS market, where affinity platforms drive near-term revenue, mapping platforms expand resolution, and true sequencing platforms define long-term disruption potential