Executive Summary / Key Takeaways

• Seer, Inc. is pioneering deep, unbiased proteomics at scale, leveraging its proprietary engineered nanoparticle (NP) technology to deliver unprecedented biological insights, a critical differentiator against traditional targeted and less scalable mass spectrometry approaches.
• The launch of the Proteograph ONE Assay and SP200 Automation Instrument in 2025 significantly enhanced throughput and precision, enabling large-scale population studies (e.g., 20,000 samples with Korea University) that were previously impractical, marking a new paradigm in proteomics research.
• Despite macroeconomic uncertainties, including government funding challenges and CapEx constraints, Seer demonstrated strong operational momentum in the first nine months of 2025, shipping nearly three times as many instruments as in all of 2024 and seeing a record number of customer publications validating its platform.
• Seer maintains a robust balance sheet with approximately $251 million in cash, cash equivalents, and investments as of September 30, 2025, which management believes is sufficient to reach cash flow breakeven, while also actively engaging in a share repurchase program.
• The company's 2025 revenue guidance of $17 million to $18 million (24% growth at midpoint) is tempered by ongoing external pressures, with revenue likely to be in the lower half of the range, but long-term gross margin targets of 70-75% reflect confidence in the scalability and value of its technology.

The Dawn of Deep, Unbiased Proteomics

Seer, Inc. (NASDAQ:SEER) stands at the forefront of a scientific revolution, dedicated to decoding the intricate biology of the proteome to advance human health. Founded in 2017, the company has strategically positioned itself as a pioneer in deep, unbiased proteomics at scale, a field critical for understanding disease mechanisms and accelerating precision medicine. This mission is powered by its innovative Proteograph Product Suite, an integrated solution that combines proprietary engineered nanoparticles, streamlined automation, optimized consumables, and advanced analytical software. This comprehensive platform enables researchers to access an unprecedented breadth of the proteome, from highly abundant to low-abundance proteins, overcoming limitations that have historically plagued mass spectrometry-based proteomics.

The industry landscape for proteomics and genomics technologies is rapidly evolving, with a clear trend towards multiomic studies that integrate genetic and proteomic data. As human genetics research increasingly moves from sequence to function, proteomics is becoming an essential complement to genomics, driving demand for advanced tools. Seer's strategic focus is on expanding its user base, enhancing access to its technology, driving larger cohort studies, and continuously innovating its product offerings. This strategy is designed to capitalize on the growing recognition of unbiased proteomics as a superior method for discovery, particularly in large-scale research.

Seer's competitive positioning is distinct. Traditional targeted proteomics approaches, such as those offered by SomaScan (now part of Thermo Fisher ) or Olink (OLK), have historically enabled large-scale studies but are inherently biased, focusing on a predefined set of proteins and prone to epitope effects due to protein variants. In contrast, Seer's Proteograph Product Suite provides an untargeted, unbiased view of the proteome, revealing novel biological insights that targeted methods often miss. The company also competes with other mass spectrometry providers like Agilent Technologies (A) and Bruker (BRKR), but its integrated workflow and nanoparticle technology offer unique advantages in sample preparation and data quality. Larger, diversified life science tools companies like Thermo Fisher Scientific and Illumina , while formidable in their broader market reach and financial resources, do not offer the same specialized, unbiased, and scalable proteomic workflow that Seer has developed.

Technological Edge and Innovation Driving Discovery

Seer's core technological differentiation lies in its proprietary engineered nanoparticle (NP) technology, which forms the foundation of the Proteograph Product Suite. This technology addresses the long-standing challenge of dynamic range in plasma proteomics, enabling the deep and unbiased interrogation of biological samples. The tangible benefits of this technology are significant and quantifiable.

The latest iteration, the Proteograph ONE Assay and SP200 Automation Instrument, launched in May 2025, represents a transformative leap. This new workflow has more than doubled throughput to over 1,000 samples per week, significantly improving scalability. It also reduces assay run time by roughly 30% compared to the previous Proteograph XT, bringing it down to approximately 4.5 hours, making it feasible within a standard workday. Crucially, the Proteograph ONE enables the identification of up to 10 times more proteins than traditional mass spectrometry workflows, achieving industry-defining precision. This translates into a meaningful reduction in cost per sample for the full workflow, making large-scale studies economically viable.

Further enhancing its platform, Seer also launched the Proteograph DIRECT assay in Q2 2025, which allows customers to run cell and tissue samples on the SP200 instrument. This assay drastically reduces manual processing time to just 60 minutes for AV samples without compromising depth or reproducibility. Complementing the hardware and consumables, the upgraded Proteograph Analysis Suite (PAS) software, introduced in 2024, has reduced data analysis time by over 95%, significantly accelerating end-to-end workflows. Seer currently offers over 10 Proteograph protocols for diverse sample types, including non-human plasma, serum, conditioned media, cerebrospinal fluid, and dried blood samples, demonstrating its versatility.

For investors, these technological advancements are paramount. They create a strong competitive moat by offering unparalleled depth, scale, and reproducibility in proteomics, directly addressing the unmet needs of researchers. This differentiation allows Seer to command a premium for its solutions and drives higher consumable pull-through, contributing to its long-term gross margin target of 70% to 75%. The ability to enable large-scale studies, such as the 20,000-sample Korea University project and the 10,000-sample Discovery Life Sciences study, positions Seer as an essential partner in groundbreaking research, potentially leading to novel biomarker discovery and advancements in precision medicine. The company's continuous R&D investment, exemplified by these new product launches and software enhancements, ensures its leadership in a rapidly evolving scientific field.

Financial Performance and Strategic Execution

Seer's financial trajectory reflects its early-stage commercialization phase, characterized by significant investments in R&D and commercial infrastructure, leading to operating losses. For the nine months ended September 30, 2025, total revenue increased by 22% to $12.38 million, compared to $10.17 million in the same period of 2024. This growth was primarily driven by higher product sales and service revenue. Product revenue for the nine months ended September 30, 2025, reached $8.37 million, a 32% increase year-over-year, while service revenue grew by 66% to $2.91 million. In the third quarter of 2025, total revenue was $4.12 million, a modest 2% increase from $4.03 million in Q3 2024, indicating some near-term stabilization.

Gross profit for the nine months ended September 30, 2025, increased by 25% to $6.28 million, with a gross margin of 51% in Q3 2025, up from 48% in Q3 2024. This improvement was attributed to a higher mix of consumable and service revenue. While gross margins are expected to fluctuate quarterly, management projects full-year 2025 gross margins to be in the range of 50% to 53%, with a long-term target of 70% to 75% at scale, underscoring the inherent profitability potential of its technology and recurring consumable sales.

Operating expenses have seen disciplined management. For the nine months ended September 30, 2025, research and development (R&D) expenses decreased by 10% to $34.13 million, and selling, general, and administrative (SG&A) expenses decreased by 25% to $32.76 million. These reductions were largely due to lower stock-based compensation and allocated costs. Despite these efficiencies, the company reported a net loss of $57.61 million for the nine months ended September 30, 2025, compared to $64.86 million in the prior year period.

Seer maintains a strong liquidity position, ending Q3 2025 with approximately $251.20 million in cash, cash equivalents, and investments. Management believes this capital is sufficient to fund operations for at least the next twelve months and to reach cash flow breakeven.

Net cash used in operating activities for the nine months ended September 30, 2025, was $33.60 million, with a free cash flow loss of approximately $35.1 million for the same period. The company anticipates a full-year 2025 free cash flow loss in the range of $40 million to $45 million. Seer has also actively engaged in a share repurchase program, buying back approximately $22 million of its Class A common shares by September 30, 2025, reducing total shares outstanding by about 14%, reflecting management's belief in a significant dislocation in its share price.

Outlook, Risks, and Competitive Dynamics

Seer's outlook for 2025 projects revenue in the range of $17 million to $18 million, representing 24% year-over-year growth at the midpoint. However, management anticipates revenue will likely fall in the lower half of this range due to persistent macroeconomic headwinds. These include ongoing budget constraints for customers, particularly in academic and government sectors (which accounted for approximately 30% of 2024 revenue and 40% year-to-date in 2025), and significant uncertainty surrounding NIH funding. The recent government shutdown further exacerbated customer uncertainty, potentially delaying grant funding and impacting Q4 shipments. Evolving tariff implementations and drug pricing control proposals also introduce volatility for commercial customers.

Despite these external pressures, Seer is experiencing strong internal tailwinds. The company shipped nearly three times as many instruments in the first nine months of 2025 as in all of 2024, demonstrating growing adoption. The Seer Technology Access Center (STAC) continues to be a crucial driver, with over two-thirds of Q3 2025 instrument shipments going to former STAC customers. The Strategic Instrument Placement Program (SIPP) also helps capital-constrained customers access the technology. Furthermore, the expanded partnership with Thermo Fisher Scientific (TMO), which yielded its first joint sale in Q3 2025, is expected to enhance commercial reach and drive adoption of the Proteograph Product Suite alongside Orbitrap Astral mass spectrometers.

The competitive landscape remains intense. While larger players like Thermo Fisher and Illumina (ILMN) possess greater financial resources and broader portfolios, Seer's technological superiority in deep, unbiased proteomics is a key differentiator. Head-to-head comparative studies, such as one led by Professor Josh Coon, have shown Seer's technology outperforms in detecting low-abundance proteins, maintaining low noise levels, and achieving superior measurement completeness. A study from the Genes & Health cohort highlighted the Proteograph's unique ability to detect protein variants and pQTLs missed by affinity-based methods, underscoring its unparalleled biological insight. This technological edge, coupled with a growing body of customer publications (a record 13 in Q3 2025, totaling 66 to date), is creating a "flywheel effect" of validation and adoption.

Key risks for Seer include its reliance on single suppliers for critical components and instrument manufacturing (e.g., Hamilton Company), which could lead to supply chain disruptions. Product defects or errors in its complex technology could damage its reputation and hinder market adoption. International expansion exposes the company to regulatory, legal, and economic risks, including data privacy laws and trade restrictions. The company's ability to obtain and enforce intellectual property protection is also crucial, as challenges to its patents could impair its competitive position. The ongoing uncertainty in government funding and broader macroeconomic volatility could continue to impact customer spending and delay the realization of its commercialization goals.

Conclusion

Seer, Inc. is a compelling investment story centered on its pioneering role in deep, unbiased proteomics at scale. The company's proprietary Proteograph Product Suite, particularly the newly launched Proteograph ONE and SP200, represents a significant technological leap, enabling unprecedented throughput, precision, and depth in proteomic analysis. This innovation is unlocking novel biological insights and facilitating large-scale population studies, positioning Seer as a critical enabler of the next generation of precision medicine and therapeutic discovery.

Despite persistent macroeconomic headwinds and funding uncertainties, Seer's operational momentum, evidenced by strong instrument shipments and a rapidly growing body of scientific validation, underscores the increasing market acceptance and impact of its technology. The company's robust balance sheet provides a strong foundation to navigate these challenges and continue strategic investments in R&D and commercial expansion, with a clear path towards cash flow breakeven. While competitive pressures are real, Seer's unique technological differentiators and strategic partnerships are solidifying its leadership in a specialized, high-growth segment of the life sciences market, making it a noteworthy consideration for discerning investors seeking exposure to the future of proteomics.