Nautilus Biotechnology, Inc.

conference call. At this time, all participants are in a listen-only mode. After the speaker's presentation, there will be a question and answer session. To ask a question during the session, you will need to press star 11 on your telephone. You will then hear an automated message advising your hand is raised. To withdraw your question, please press star 11 again. Please be advised that today's conference is being recorded. I would now like to hand the conference over to your speaker today, Jianyi Investor Relations. Please go ahead.

Thank you. Earlier today, Nautilus released financial results for the quarter ended September 30, 2025. If you haven't received this news release or if you'd like to be added to the company's distribution list, please send an email to investorrelations at nautilus.bio. Joining me today from Nautilus are Sujil Patel, co-founder and CEO, Farag Malik, co-founder and chief scientist, Ken Suzuki, chief marketing officer, and Anna Mowry, chief financial officer. Before we begin, I'd like to remind you that management will make statements during this call that are forward-looking within the meeting of the federal securities laws. These statements involve material risks and uncertainties that could cause actual results or events to materially differ from those anticipated. Additional information regarding these risks and uncertainties appears in the section entitled forward looking statements in the press release Nautilus issued today. Except as required by law, Nautilus disclaims any intention or obligation to update or revise any financial or product pipeline projections or other forward looking statements, whether because of new information, future events, or otherwise. This conference call contains time-sensitive information and is accurate only as of the live broadcast on October 28, 2025. With that, I'll turn the call over to Sejal.

Thanks, Jian, 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 Neural 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 two other exciting partners. The first is the Allen Institute for Brain Science. As highlighted in our July 30th 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 WorldHupo 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's also an eminent proteomics KOL and recently served as president of USHupo. Our session with Birgit at WorldHupo 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 peptides. 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. 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 telepathies. 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 discoveries. 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 platforms. 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 broad-scale 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 broad scale asset 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 broad-scale 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 broad-scale launch. We're confident that broad scale 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? 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 interviews 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 one customer commented that the Nautilus platform, quote, has the potential to replace a major portion of mass spectrometry and proteomics, end quote. 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 describe 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?

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 costs 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 two 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 Tao 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.

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 TAO 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 TAO. We're preparing to showcase externally generated TAO data at WorldHupo 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 toward the new broad-scale 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?

As a reminder, to ask a question, please press star 11 on your telephone and wait for your name to be announced. To withdraw your question, please press star 11 again. Please stand by while we compile the Q&A roster. Our first question comes from Dan Brennan with TD Cowan. Your line is open.

Hi, thank you. This is William Ruby on for Dan Brennan. Just a couple questions. First, I'm 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 just 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. Thank you.

Hi, 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.

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 you see, what we talked about on the script was that we intend to launch our early access program in the first half initially with TAO and our proteoform panel with TAO. And then in the second half, we'll expand that early access to include our broad scale 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, you know, we continue to state that by the end of 2026, we expect a launch of our broad scale capabilities. And this is that early access and then launch model is a model that we'll use for subsequent proteoforms and subsequent versions of broad scale 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 started with Tau and with BroadScale. With Tau, obviously, the pipeline build in earnest really just began as we released that pre-print last quarter, meaning Q2 of 2025, and started to talk to partners about the capabilities of our product. As we mentioned in prepared remarks, we intend to, at the beginning or the first half of 2026, launch early access in a formal manner for those TAO capabilities. With that coming, we're in the process of finalizing our product verification and validation. We're in the process of talking to and building the top of the funnel for those TAO capabilities. and we're starting to think through the first commercial hires, which we would expect the first, you know, 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 TAO services initially, and then broad scale as we move on to the second half of the year.

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