Nautilus (NAUT) Q3 2025 Earnings Call Transcript

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Date

Tuesday, Oct. 28, 2025, at 8:30 a.m. ET

Call participants

• Chief Executive Officer — Sujal Patel
• Chief Marketing Officer — Kentaro Suzuki
• Chief Financial Officer — Anna Mowry

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Takeaways

• Total Operating Expenses -- $15.5 million for the third quarter of 2025, reflecting focused cost management and reduced development costs.
• Research and Development Expenses -- $9.6 million in the third quarter of 2025, down from $12.3 million in Q3 2024, due to lower development costs and improved efficiency in personnel, laboratory, and services spend.
• General and Administrative Expenses -- $5.9 million in the third quarter of 2025, reduced from $6.8 million in the prior-year quarter, primarily from lower stock-based compensation expense.
• Net Loss -- Net loss was $13.6 million for the third quarter of 2025, compared to $16.4 million in Q3 2024.
• Ending Cash, Cash Equivalents, and Investments -- $168.5 million in cash, cash equivalents, and investments as of the third quarter of 2025, supporting a forecasted cash runway through 2027.
• Q3 Cash Burn -- $11.0 million cash burn in the third quarter of 2025, benefitting from lower operating expenses.
• Expense Outlook -- Q3 spending was the lowest point this year, with future quarters expected to increase as commercialization activities ramp up.
• Commercialization Timeline -- Early access program for the Tau proteoform assay set to launch in the first half of 2026; broadscale commercial platform launch anticipated in late 2026.
• Partnerships -- Announced key collaborations with the Allen Institute for Brain Science and the Buck Institute for Research on Aging, generating externally validated Tau proteoform data.
• Platform Validation -- Dr. Birgit Schilling to publicly present Tau data generated on the Nautilus platform at the World HUPO Conference in November, marking the first external scientific presentation using their assay.
• Pipeline Development -- Expanded pipeline includes academic centers, nonprofit institutes, and biopharma companies, with growing interest in proteoform-based precision biomarkers.
• Assay Configuration Advancement -- Achieved a key milestone with a new broadscale assay configuration, ensuring compatibility with previously incompatible affinity reagent probes; full probe library testing planned in Q4 and Q1 2026.
• Market Research -- Completed a detailed market study involving over 250 decision-makers from academic and industry segments in North America and Europe; data indicated customers "expect and are willing to pay a premium," according to Kentaro Suzuki for the Nautilus platform.
• Revenue Outlook -- Management stated only limited near-term services revenue is expected from early Tau assay engagement and that "we don't expect meaningful services revenue from these engagements in 2026."

Summary

Nautilus Biotechnology (NASDAQ:NAUT) reported significant progress in external validation of its proteomics platform, highlighted by new Tau assay data set for external presentation at a leading scientific conference. The company confirmed its forecasted cash position supports operations through 2027 and outlined a two-stage commercialization plan, beginning with early access in the first half of 2026 and a broad commercial launch by the end of 2026. Robust interest from academic, nonprofit, and biopharma partners, combined with data-supported market enthusiasm for both technical and economic differentiation, underscores management's positioning for upcoming commercial activities.

• Anna Mowry stated, "we expect Q3 will be a low point in our spending and future quarters will increase as product and market development activities ramp up."
• Customers valued the Nautilus platform on par with high-end mass spectrometry systems, with willingness to pay a premium directly attributed to broad-scale and single-molecule proteoform capabilities.
• Management projected that early access participation would primarily generate platform validation and scientific publications, rather than significant revenue, in 2026.
• Growth in the collaborator pipeline during the third quarter of 2025 follows the publication of a preprint in the second quarter and new strategic alliances, supporting management's expectations for future commercial and scientific engagements.

Industry glossary

• Proteoform: A specific molecular variant of a protein resulting from genetic variation, alternative splicing, or post-translational modifications, central to biomarker discovery in proteomics.
• Tau: A protein associated with neurodegenerative diseases such as Alzheimer's, for which distinct proteoforms can indicate disease state and progression.
• Affinity Reagent Probe: A molecule designed to bind selectively to a target protein or proteoform, enabling high-specificity detection within assay platforms.
• Broadscale Assay Configuration: Refers to Nautilus’s assay setup optimized for large-scale, comprehensive profiling of complex proteomes using an expanded probe library.
• HUPO (Human Proteome Organization): An international scientific organization advancing global proteomics research, with its World HUPO Conference serving as a forum for scientific data dissemination.

Full Conference Call Transcript

Sujal Patel: Thanks, Ji-Yon, and thank you all for joining us. Q3 was another important quarter for Nautilus. We made meaningful progress across our scientific platform and operational priorities as we continue our disciplined path toward commercialization. Last quarter, we published a preprint showcasing our iterative mapping method and demonstrating the power of our platform to measure proteoforms, distinct forms of proteins with unprecedented resolution. That manuscript was accompanied by an announcement of Tau focused collaborations with investigators from the Neuro Stem Cell Institute and with Joel Blanchard's lab at Mount Sinai Medical Center. These collaborators were central to generating the intriguing biological data shared in that manuscript.

In addition to these partnerships, I'd like to call attention to 2 other exciting partners. The first is the Allen Institute for Brain Science. As highlighted in our July 30 press release, that collaboration aims to examine how Tau proteoforms vary across brain regions as a function of disease severity. Ultimately, such projects may enable the use of proteoform biomarkers to predict the course of Alzheimer's disease. We're excited to have already begun generating the first data sets from their samples. One other key collaborator is the Buck Institute for Research on Aging.

As a world leader in aging research, they have deep experience in Alzheimer's disease research and are excited to examine how Tau proteoforms contribute to disease progression and therapeutic efficacy. I'm particularly thrilled to share that Dr. Birgit Schilling, one of our collaborators at the Buck Institute, will be presenting her results at the Human Proteome Organization's World HUPO Conference in November marking the first public presentation of externally generated Tau data measured on the Nautilus platform. In addition to being an acclaimed aging researcher, she is also an eminent proteomics KOL and recently served as President of U.S. HUPO.

Our session with Birgit at World HUPO will highlight both key technical aspects of the Tau assay such as reproducibility and also intriguing biological findings that were only possible using the Nautilus platform. I'd like to call attention to the fact that the results in our manuscript and the results that Birgit will be sharing are based on real-world biological samples, not only model samples composed of recombinant proteins or peptide. We believe our presentation at HUPO will not only validate the technical readiness of our assay, but will also underscore the potential for our platform to drive meaningful biological insight, something we consistently hear is a top priority for researchers in this space.

We view the results from our early partnerships as clearly demonstrating our platform's unique ability to measure proteoforms at an unprecedented level of precision and resolution. This is especially important for targets like Tau where the combination of isoforms and post-translational modifications have a profound impact on disease progression. We expect that the Nautilus platform's unique ability to quantify complex mixtures of proteoforms at the single-molecule level will prove an important tool for driving biological insight. Collaborations with institutions like the Buck and the Allen institutes are emblematic of the caliber of researchers and institutions that are now engaging with Nautilus. This quarter, our pipeline of potential collaborators has expanded significantly, including academic centers, nonprofit institutes and biopharma companies.

These researchers are eager to explore how Nautilus can bring new clarity to neurodegenerative disease biology and also eager to explore proteoform-based precision biomarkers for Alzheimer's disease and related tauopathies. These researchers also understand that studying Tau requires resolution beyond what traditional platforms can offer and recognize that our approach is uniquely suited to identify the modified forms of Tau that may drive disease progression. We're also seeing increased interest from additional partners eager to expand into new disease areas and novel proteoform targets reflecting both the maturity of our platform and the unique insights it enables. The conversations we're having are with premier researchers and institutions at the forefront of translating molecular insights into impactful diagnostic and therapeutic advances.

The growing engagement we're seeing reinforces our belief that Nautilus is becoming a key enabling technology for the next generation of biological discovery. We anticipate that several of these discussions will lead to active engagements when we launch our early access program in the first half of 2026. Initially, customers will gain streamlined access to our Tau proteoform assay. Select partners will be able to submit samples, receive data and provide feedback, similar to our current engagement with the Allen Institute. These early engagements will primarily focus on generating high-quality data and validating our platform. We expect only limited revenue in the near term.

However, this validation is essential for building momentum and opening broader commercial opportunities, including the expansion of our assay for other proteoforms of interest. Over time, we'll expand our early access to offer support for both targeted proteoform assays and for broadscale proteomic studies. Our aim is to make each early engagement an opportunity to build credibility, momentum and operational readiness ahead of our commercial launch. On the technology front, we made steady progress in Q3 transitioning to our new broadscale assay configuration to better align with our growing probe library and improve platform performance. Early results have been promising and we expect this configuration to enable our broad-scale commercial launch in late 2026.

Briefly, assay configuration change efforts were focused on better aligning assay design with the characteristics of our expanding probe library, improving probe yield and overall platform performance. One of the most significant areas of change was in the flow cell and associated assay reagents. Together, these changes were designed to reduce technical risk and enable higher performance as we scale toward a more comprehensive view of the proteome. A key milestone of our broadscale assay configuration change was achieved in Q3 demonstrating that affinity reagent probes previously incompatible with our old assay configuration are compatible with the new configuration.

In Q4 of this year and Q1 of 2026, we plan to test the whole probe library with this new configuration to better understand performance and finalize the steps needed for broadscale's launch. We're confident that broadscale will drive long-term scalability and value for Nautilus. Lastly, we continue to be highly intentional in how we invest our resources. In Q3, we reduced expenses quarter-over-quarter, reflecting a more focused operating model aligned with our top priorities. This operational discipline is an important part of how we're extending our runway even as we move closer to commercialization.

Taken together, the progress we've made in Q3 moves us closer to realizing the promise of single molecule proteomics, a future where researchers can decode biology with a level of precision and resolution that is simply not possible today. We're proud of the scientific and technical advances made this quarter and grateful to our team and collaborators who continue to push the boundaries of what's possible. As always, I want to thank our scientific and engineering teams for their continued dedication. The work they're doing is not only technically challenging, it's foundational to the future of proteomics.

With that, I'll hand the call over to Ken, our Chief Marketing Officer, to share key insights from our recent voice of the customer and market research work. Ken?

Kentaro Suzuki: Thanks, Sujal, and good morning, everyone. Over the past several months, our teams have been focused on sharpening our marketing strategy by developing a deep understanding of our customers, their challenges with existing technologies, goals for next generation solutions and how the Nautilus platform can uniquely address their needs. In the third quarter, we completed an extensive market study involving more than 250 decision-makers across North America and Europe spanning academic institutions, pharma, biopharma and leading proteomics organizations. These participants represent our core target segments and are highly familiar with both mass spectrometry and affinity-based technologies. Through a combination of detailed qualitative [ in-reviews ] and deep quantitative analysis, we built a rigorous and data-rich view of our market opportunity.

Three clear themes emerged. First, customers viewed the Nautilus platform as uniquely differentiated from current mass spectrometry and affinity-based technologies. They highlighted our iterative mapping approach as delivering an unmatched combination of protein coverage, reproducibility and sensitivity. In particular, customers were most drawn to our ability to achieve both broad proteome coverage and deep single molecule proteoform level resolution, a capability that only iterative mapping can deliver. Our competitive differentiation is stronger than ever. As a former General Manager of mass spectrometry at Agilent, I found it especially validating when 1 customer commented that the Nautilus platform "has the potential to replace a major portion of mass spectrometry and proteomics".

Second, our research confirmed that customers both expect and are willing to pay a premium for our solution. The ability of iterative mapping to provide broad scale and proteoform level insights drove particularly strong enthusiasm and willingness to invest in our solution. Combined with the platform's reproducibility, sensitivity and simple AI-ready output; customers valued our instrument on par with high-end mass spectrometry systems, a strong endorsement in an already premium segment. Finally, we heard a clear and consistent message of eagerness to engage with Nautilus. Many customers described current technologies as limiting, constrained in performance, lacking cross-platform agreement and often complex to use.

They are actively seeking a new class of measurement technology to complement or replace their existing tool sets. After decades of experience introducing new products, I'm encouraged by the strength of this product market fit and by our customers' enthusiasm to begin evaluating the Nautilus platform. We are channeling this confidence as we plan for our early access program beginning with the Tau proteoform assay in the first half of 2026. I look forward to continue sharing our progress as we transition towards our commercial phase. Next, I'll hand over the call to Anna to walk through our financials. Anna?

Anna Mowry: Thanks, Ken. For the third quarter of 2025, total operating expenses were $15.5 million, down from $19.1 million in the same quarter of 2024. This 19% year-over-year decrease reflects our continued focus on expense management, operating efficiency and lower development costs overall. Our stock-based compensation expense also declined meaningfully year-over-year. Research and development expenses for the third quarter of 2025 were $9.6 million, down from $12.3 million a year ago. This year-over-year reduction was driven by lower development cost as well as improved operating efficiency in personnel, laboratory and services spend. General and administrative expenses were $5.9 million, down from $6.8 million in Q3 2024 driven largely by reduced stock compensation expense.

Net loss for the quarter was $13.6 million compared to $16.4 million in the prior year period. We ended the quarter with $168.5 million in cash, cash equivalents and investments. Cash burn in Q3 was $11.0 million reflecting the benefit of lower operating expenses. We continue to project a cash runway extending through 2027 providing ample time to advance platform development and early-stage commercial activities. Looking ahead, we anticipate that total operating expenses for the full year 2025 will come in below what we saw over the past 2 years. With that being said, we expect Q3 will be a low point in our spending and future quarters will increase as product and market development activities ramp up.

As for our Tau early access program, the first customer engagements are likely to be with academic KOLs that need access to the platform and initial data sets in order to support their grant applications. We believe these first internally funded services engagements will lead to revenue engagements over time, but more importantly, publications, additional grant applications and potentially instrument orders. We are excited by the shift towards commercially oriented activities, but we don't expect meaningful services revenue from these engagements in 2026. Back to you, Sujal.

Sujal Patel: Thanks, Anna. As you've heard throughout today's call, Q3 was a quarter of continued execution and meaningful progress for Nautilus. We advanced our Tau proteoform assay, built momentum with prospective collaborators and are on track to launch our early access program in the first half of 2026 beginning with Tau. We're preparing to showcase externally generated Tau data at World HUPO in November, a milestone that reflects years of investment in scientific and technical innovation. As demonstrated by our excitement and ability to expand our collaborative work, Nautilus' doors are open today for partners who are interested in funding the development of new proteoform assays and shaping the future of proteomics.

We also made steady progress towards the new broadscale assay configuration that will support our commercial launch. In addition, our disciplined operations and spending have us ending the quarter with a strong balance sheet and clear line of sight to our strategic goals. As we close, I want to step back and emphasize something fundamental. Our platform is as disruptive today as it was when we first set out to build it and now we have even more external validation to back that up. Iterative mapping represents a completely new class of measurement, different from anything else in the market, delivering proteome and proteoform insights that existing technologies simply cannot match.

Our extensive market research and voice of the customer work encompassing more than 250 interviews with representative customer groups makes it clear that the market recognizes our differentiation. Customers consistently affirm that what we're building will reshape the landscape. This strong validation gives us tremendous confidence in both our technology and the commercial opportunity ahead. I'm incredibly proud of what the team has accomplished; the science we're advancing, the platform we're building and the opportunities ahead. Our foundation is strong and our mission has never been more focused. Thank you again for joining us today. With that, we'll open the call for questions. Operator?

Operator: [Operator Instructions] Our first question comes from Dan Brennan with TD Cowen.

William Ruby: This is William Ruby on for Dan Brennan. Just a couple of questions. First, just wondering how we should think about the level of OpEx investment you'll need to make heading into the launch next year. And I know you touched on it a good amount on the call, but if you could just go into a little bit more detail on the funnel that you're building out of early access coming into next year.

Anna Mowry: William, this is Anna. I can speak to the first one. From an OpEx standpoint, we're, as I said in the prepared remarks, expecting that from our low point here in Q3 we are anticipating that spend will increase as we get closer to commercialization. As you might expect, I don't have an outlook yet for 2026, but you can extrapolate from our guidance that we have cash through 2027 and I would anticipate some steady step-up between now and the end of 2027.

Sujal Patel: And William, this is Sujal. Let me take the second half of your question, which is the funnel. So let me first sort of describe just in a little more detail how we would expect next year to unfold. And so what we talked about on the script was that we intend to launch our early access program in the first half initially with Tau and our proteoform panel with Tau and then in the second half, we'll expand that early access to include our broadscale proteomic capabilities. And that sort of setup will lead to a launch of each of those things after that early access period, that official launch.

And we continue to state that by the end of 2026, we expect a launch of our broadscale capabilities. And that early access and then launch model is a model that we'll use for subsequent proteoforms and subsequent versions of broadscale and so forth as we move beyond into future years. So in terms of the pipeline build, pipeline build is occurring for both of those different products and use cases, proteoform starting with Tau and with broadscale. With Tau, obviously the pipeline build in earnest really just began as we released that preprint last quarter meaning Q2 of 2025 and started to talk to partners about the capabilities of our product.

And as we mentioned in the prepared remarks, we intend to at the beginning or the first half of 2026 launch early access in a [ funnel ] manner for those Tau capabilities. And so with that coming, we're in the process of sort of finalizing our product verification and validation. We're in the process of talking to and building the top of the funnel for those Tau capabilities.

And we're starting to think through the first commercial hires, which we would expect the first -- we have business development and scientific affairs types of headcount today, but we would expect that in the first quarter we would make our first official hire on the direct sales side as well to build capacity for the Tau services initially and then broadscale as we move on to the second half of the year.

Operator: Thank you. This concludes today's question-and-answer session and today's conference call. Thank you for participating. You may now disconnect.

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