Quantum-Si Conference Call Summary Company Overview - **Company**: Quantum-Si (NasdaqGM:QSI) - **Industry**: Life Sciences Tools and Diagnostics - **Technology**: Utilizes semiconductor chip technology for single-molecule protein sequencing with products including the Platinum instrument and QSI Cloud software [3][4] Key Points and Arguments Product Portfolio and Technology - **Current Products**: The first-generation technology includes the Platinum and Platinum Pro instruments, which have been in the market for about three years [4] - **Business Model**: Operates on a razor-razor blade model where customers purchase the machine and consumables for sample preparation and sequencing [4] - **Upcoming Product**: The Proteus platform represents a significant architectural change, moving optics from consumables to the machine, allowing for higher sequencing output and lower-cost consumables [5][15] Financial Performance and Strategy - **Recent Earnings**: The company has adapted to NIH headwinds by offering alternative purchasing options for the Platinum machine, resulting in 12 machines sold under this program, with over half going to academia [6] - **Publications**: Five publications have been released this year, indicating a strong pipeline and market development [6] - **Cash Position**: Ended Q3 2025 with over $230 million in cash, providing a runway into Q2 2028, which includes 18 months post-Proteus launch [44][46] Proteus Development and Launch Timeline - **Milestones**: Completed sequencing on over 50 runs of the Proteus prototype, achieving this milestone ahead of schedule [7][8] - **Launch Timeline**: Expected to launch Proteus by the end of 2026 [21][22] - **Early Access Program**: Targeting big centers with core labs for testing and comparison against existing technologies [26][28] Pricing Strategy - **Price Range**: Anticipated pricing for Proteus is between $300,000 and $500,000, reflecting its advanced capabilities compared to the current Platinum device priced at $125,000 [23][24] - **Market Accessibility**: The pricing strategy aims to balance value capture with accessibility to avoid constraining the number of potential users [25] R&D and Technological Advancements - **AI and Binding Kinetics**: The integration of AI tools has accelerated the development of engineered protein recognizers, enhancing the ability to achieve full proteome coverage [30][31] - **Proteome Coverage Goals**: Aiming to demonstrate coverage of all 20 amino acids by 2026, which would enable advanced applications in single amino acid variants and post-translational modifications (PTMs) [33] Commercialization Strategy - **Sales Strategy**: Considering various sales models for Proteus, including trade-ins for existing Platinum users, while leaning towards capital sales [39][40] - **Long-term Focus**: Emphasis on capital efficiency and targeted investments to support the Proteus launch and subsequent commercialization efforts [46][47] Additional Important Insights - **Engineering and Chemistry Hurdles**: Early data from Proteus shows improvements across all metrics compared to the Platinum machine, indicating a de-risked program moving towards commercialization [10][12] - **Controlled Cleavage Technology**: Future versions of Proteus may incorporate controlled cleavage technology to enhance sequencing capabilities [41][43] - **Strategic Opportunities**: Open to exploring strategic opportunities and technologies that align with Quantum-Si's goals, while maintaining focus on the Proteus launch [47]

Core Insights - The presentation aims to provide an overview of the company's advancements in proteomics and the associated challenges in understanding the complexity of the proteome [1] - The focus is on the Proteus program, which represents the majority of the company's R&D investment, highlighting its significance in enhancing performance [1] Group 1: Technology and R&D - The company is investing heavily in the Proteus program, which is central to its current R&D efforts [1] - There are also modest investments in long-term technology development, indicating a balanced approach to immediate and future innovations [1] Group 2: Future Developments - Upcoming discussions will include plans to expand to 20 amino acids, with details on the timeline for achieving this goal [2]

Quantum-Si Investor Day Summary Company Overview - **Company**: Quantum-Si (NasdaqGM:QSI) - **Event**: 2025 Investor Day - **Date**: November 19, 2025 Industry Context - **Industry**: Proteomics - **Market Size**: Proteomics is described as a massive market with various segments including academic research, pharma, biotech, defense, and agriculture [2][3][4] - **Complexity**: The proteome consists of approximately 20,000 proteins, but the presence of post-translational modifications and isoforms leads to millions of proteoforms, making it a complex challenge [2][3] Key Points and Arguments Proteus Technology - **Proteus Program**: The majority of R&D investment is focused on the Proteus program, which aims to enhance protein sequencing capabilities [2][10] - **Architecture Change**: The Proteus architecture simplifies the imaging system, allowing for a scalable consumable with up to 80 million wells, compared to 2 million in the previous Platinum system [11][12] - **Automation and Affordability**: The new system aims to automate workflows and reduce costs, making deep protein analysis more accessible [7][12] Performance Improvements - **Sequencing Output**: Proteus is expected to produce 1.8 times more alignments per well compared to Platinum, with a significant increase in the number of wells [19][21] - **Sensitivity**: The signal-to-noise ratio (SNR) of Proteus is about twofold higher than that of Platinum, enhancing the detection of binding events [23] - **Long-Range Structural Information**: Proteus can provide deep sequencing capabilities, crucial for understanding post-translational modifications and variants [22] Future Roadmap - **Launch Timeline**: The first integrated systems are expected to be completed in Q1 2026, with a product launch planned for the end of 2026 [25][26] - **Detection of Amino Acids**: The goal is to detect all 20 amino acids by 2027, with 18 expected to be available at the launch of Proteus [48][62] - **AI and Data Utilization**: The company is leveraging AI for binder design and protein structure prediction to accelerate the development of amino acid recognizers [56][62] Additional Important Insights - **Market Challenges**: The complexity of proteomics makes traditional affinity-based approaches impractical for scaling [3][4] - **Technical Risks**: The company has focused on retiring technical risks through prototypes and has demonstrated the feasibility of the new architecture [12][13] - **Investment in R&D**: The company emphasizes that most of its investment is directed towards product development that will reach the market within the next couple of years [38][64] Conclusion Quantum-Si is positioned to make significant advancements in the proteomics field with its Proteus technology, which promises to enhance sequencing capabilities, reduce costs, and improve accessibility. The roadmap indicates a clear path towards achieving the detection of all 20 amino acids, supported by innovative technology and strategic investments in R&D.

Financial Data and Key Metrics Changes - Revenue for Q3 2025 was $552,000, impacted by capital sales headwinds in the market [4][16] - Gross profit was $194,000, with a gross margin of 35% [16] - For the nine months ended September 30, 2025, revenue was $2.0 million, and gross profit was $1.0 million, with a gross margin of 52% [16][18] - Total operating expenses for Q3 2025 were $40 million, compared to $28.5 million in Q3 2024 [18] - Adjusted operating expenses for Q3 2025 were $21.4 million, down from $26.0 million in Q3 2024 [18] Business Line Data and Key Metrics Changes - The company launched an expanded set of instrument acquisition options, resulting in 12 new customers implementing the platform [5] - More than half of the new customers are in academic labs, a segment previously difficult to access due to NIH funding challenges [5] Market Data and Key Metrics Changes - The company experienced year-over-year revenue impacts due to capital market headwinds and NIH funding uncertainties [17] - The placements program has allowed access to key academic centers, with over half of placements going into academic labs [34] Company Strategy and Development Direction - The company aims to accelerate commercial adoption, deliver on its innovation roadmap, and preserve financial strength [4] - The Proteus platform is a key focus, with successful sequencing runs completed on prototype systems [9] - The company is exploring partnership opportunities to enhance development activities and expand market participation [8] Management's Comments on Operating Environment and Future Outlook - Management expressed optimism about early traction with the placement program despite ongoing capital market challenges [13] - The company anticipates modest improvement in Q4 2025, but not a significant upswing compared to historical trends [40] - There is uncertainty regarding NIH funding due to the government shutdown, but proposals indicate a potential retention of funding levels [41][42] Other Important Information - The company has a strong balance sheet with $230.5 million in cash and investments as of September 30, 2025 [20] - A Form S-3 shelf registration statement for $300 million was filed to support business initiatives [22] - Management and board collectively hold approximately 18% of the total outstanding stock, indicating strong investment in the company's success [24] Q&A Session Summary Question: Updates on the investor day and Proteus sequencer development - The investor day on November 19 will provide updates on Proteus, including early sequencing data and key milestones for 2026 [28][29] Question: Involvement in DARPA's PRESS program - The company is aware of the PRESS program but does not align perfectly with its microsystem strategy [31] Question: Breakdown of placements by market segment - More than half of the placements went into academic labs, with the remainder split between pharma, biotech, and agricultural testing [34] Question: Seasonal trends from Q3 to Q4 - A modest improvement is expected in Q4 2025, but not as significant as in typical years due to various challenges [40] Question: Key hurdles to market launch of Proteus - Key hurdles include scaling from prototypes to fully integrated systems and optimizing the platform for manufacturing [44][46]

Financial Performance - Total revenue for Q3 2025 was $552,000, a decrease of 29.9% compared to $787,000 in Q3 2024[130] - Product revenue decreased by 33.9% to $505,000 in Q3 2025 from $764,000 in Q3 2024, while service revenue increased by 104.3% to $47,000[130] - Gross profit for Q3 2025 was $194,000, down 47.1% from $367,000 in Q3 2024[130] - The net loss for Q3 2025 was $35,703,000, representing a 41.0% increase from a net loss of $25,313,000 in Q3 2024[130] - Total revenue for the three months ended September 30, 2025, decreased by $0.2 million, or 29.9%, compared to the same period in 2024, while for the nine months, it increased by $0.1 million, or 6.4%[133] - Gross profit for the three months ended September 30, 2025, decreased by $0.2 million, or 47.1%, while it increased slightly for the nine months ended September 30, 2025, compared to the same periods in 2024[135] - Gross profit margin was 35.1% for the three months and 51.9% for the nine months ended September 30, 2025, compared to 46.6% and 53.1% for the same periods in 2024, respectively[136] Operating Expenses - Operating expenses increased by 40.5% to $39,967,000 in Q3 2025 compared to $28,455,000 in Q3 2024[130] - Research and development expenses for the three months ended September 30, 2025, decreased by $2.3 million, or 14.1%, while for the nine months, they increased by $0.2 million, or 0.4%[140][141] - Selling, general and administrative expenses decreased by $1.6 million, or 12.8%, for the three months ended September 30, 2025, and by $1.8 million, or 4.8%, for the nine months compared to the same periods in 2024[143][144] - Lease termination expense increased by $13.6 million for both the three and nine months ended September 30, 2025, due to a settlement agreement to terminate a lease[145] - Legal settlement expense increased by $1.8 million and $5.2 million for the three and nine months ended September 30, 2025, respectively, due to settlements related to litigation[146] Cash Flow and Liquidity - Net cash used in operating activities for the nine months ended September 30, 2025, was $78.4 million, primarily due to a net loss of $83.7 million[155] - Net cash used in investing activities for the nine months ended September 30, 2025, was $35.3 million, an increase from $26.8 million in the same period in 2024[157] - Net cash provided by financing activities for the nine months ended September 30, 2025, was $95.4 million, compared to $0.1 million for the same period in 2024[158] - As of September 30, 2025, the company had cash and cash equivalents and investments in marketable securities totaling $230.5 million[161] - The company expects to incur negative operating cash flows on an annual basis for the foreseeable future until it can scale its revenue growth[159] - The company anticipates that existing cash and cash equivalents will be sufficient to meet liquidity and capital expenditure requirements for at least the next 12 months[160] Workforce and Restructuring - The company terminated approximately 23% of its workforce as part of a restructuring program, incurring one-time cash charges of approximately $2.3 million[122] Product Development and Launches - The company launched the Platinum Pro benchtop sequencer in January 2025, with first shipments occurring in March 2025[118] - A new platform, Proteus, is expected to launch in the second half of 2026, aiming for single molecule, amino acid level resolution[120] - The company began a controlled launch of the Platinum instrument in December 2022, with a full commercial launch starting in Q2 2024[138] - The company expects gross profit margin to be variable for the foreseeable future as it continues its commercialization efforts[137] Warrant Liabilities - The change in fair value of warrant liabilities increased significantly by 1152.9% to $1,516,000 in Q3 2025 compared to $121,000 in Q3 2024[130] - For the three months ended September 30, 2025, the company recognized $1.5 million of income from the decrease in the fair value of warrant liabilities, an increase of $1.4 million or 1152.9% compared to the same period in 2024[150] - For the nine months ended September 30, 2025, the company recognized $3.9 million of income from the decrease in the fair value of warrant liabilities, an increase of $3.0 million or 327.8% compared to the same period in 2024[151] Foreign Currency Risk - The company anticipates limited activity outside the U.S. Dollar in the near term[176] - Foreign currency translation risk is not expected to have a material impact on the unaudited Condensed Consolidated Financial Statements[176] - The growth of operations and transactions outside the U.S. may increase foreign currency translation risks in the future[176] - The company has not entered into any hedging arrangements regarding foreign currency risk to date[176] - As international operations grow, the company will reassess its approach to managing currency rate fluctuations[176]

Exhibit 99.1 Quantum-Si Reports Third Quarter 2025 Financial Results Announces Successful Sequencing on Prototype Proteus Unit, Development Program Remains On-Track BRANFORD, Conn. -- (BUSINESS WIRE) -- November 5, 2025 -- Quantum-Si Incorporated (Nasdaq: QSI) ("Quantum-Si," "QSI" or the "Company"), a proteomics technology company redefining protein analysis through single- molecule detection, today announced financial results for the third quarter ended September 30, 2025. Press Release Highlights Total op ...

Alternatively, individuals can register here to receive a dial-in number and personalized PIN to participate in the call. An archived webcast of the event will be available for replay following the event. BRANFORD, Conn.--(BUSINESS WIRE)--Quantum-Si Incorporated (Nasdaq: QSI) ("Quantum-Si,†"QSI†or the "Company†), a proteomics technology company redefining protein analysis through single-molecule detection, today announced that it will report financial results for the third quarter 2025 on Wednesday, Nov ...

Core Viewpoint - Quantum-Si is seeking to raise up to $300 million in new funding, which has raised concerns among investors about potential dilution of shares [1][3][5] Group 1: Funding Plans - Quantum-Si filed a shelf registration with the SEC, indicating its intention to raise capital over time [2] - The company plans to raise up to $300 million through various types of securities, including Class A common stock, preferred stock, and debt securities [3] - The proceeds from these securities may be used for product development, commercialization, capital expenditures, and administrative expenses [4] Group 2: Market Reaction - Following the announcement, Quantum-Si's shares experienced a nearly 5% loss in value, reflecting investor concerns about potential dilutive secondary share issues [1][5] - The company's current market capitalization is $336 million, leading to fears that raising close to $300 million in equity could significantly dilute existing shares [5]

Group 1: U.S. Stock Market Overview - U.S. stock futures were higher, with Dow futures gaining over 100 points on Monday [1] Group 2: Inventiva ADR Performance - Inventiva reported losses of $(1.84) per share, significantly worse than the analyst consensus estimate of a loss of 41 cents per share [1] - The company reported quarterly sales of $5.050 million, missing the analyst consensus estimate of $5.310 million [1] - Inventiva shares dipped 5.5% to $5.72 in pre-market trading [1] Group 3: Other Stocks in Pre-Market Trading - MoonLake Immunotherapeutics saw a significant decline of 86.3% to $8.50 in pre-market trading [4] - Cellectis SA declined 10.4% to $3.01 in pre-market trading [4] - Quantum-Si Inc fell 10.1% to $1.34 in pre-market trading after filing for a mixed shelf of up to $300 million [4] - Penguin Solutions Inc decreased by 8.4% to $24.00 in pre-market trading [4] - Lithium Americas Corp declined 5.4% to $5.99 in pre-market trading after a 14% drop on Monday [4] - Platinum Analytics Cayman Ltd fell 5.3% to $16.20 in pre-market trading after a 44% increase on Monday [4] - Novo Nordisk A/S decreased by 2.9% to $54.01 in pre-market trading [4] - Lexicon Pharmaceuticals Inc declined 2.9% to $1.36 in pre-market trading, recently announcing an update on submission of additional data to the U.S. FDA regarding Zynquista® in Type 1 Diabetes [4]

Group 1: U.S. Stock Market Overview - U.S. stock futures were higher, with Dow futures gaining over 100 points on Monday [1] Group 2: Inventiva ADR Performance - Inventiva reported a loss of $(1.84) per share, significantly worse than the analyst consensus estimate of a loss of 41 cents per share [1] - The company’s quarterly sales were $5.050 million, missing the analyst consensus estimate of $5.310 million [1] - Inventiva shares fell 5.5% to $5.72 in pre-market trading [1] Group 3: Other Stocks in Pre-Market Trading - MoonLake Immunotherapeutics saw a significant decline of 86.3% to $8.50 in pre-market trading [4] - Cellectis SA declined 10.4% to $3.01 in pre-market trading [4] - Quantum-Si Inc fell 10.1% to $1.34 in pre-market trading after filing for a mixed shelf of up to $300 million [4] - Penguin Solutions Inc dropped 8.4% to $24.00 in pre-market trading [4] - Lithium Americas Corp declined 5.4% to $5.99 in pre-market trading after a 14% dip on Monday [4] - Platinum Analytics Cayman Ltd fell 5.3% to $16.20 in pre-market trading after a 44% jump on Monday [4] - Novo Nordisk A/S decreased by 2.9% to $54.01 in pre-market trading [4] - Lexicon Pharmaceuticals Inc declined 2.9% to $1.36 in pre-market trading, with an update on additional data submission to the U.S. FDA regarding Zynquista® in Type 1 Diabetes [4]