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ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

The following discussion and analysis provides information which management believes is relevant to an assessment and understanding of our consolidated results of operations and financial condition. The discussion should be read in conjunction with the Consolidated Financial Statements and Notes thereto contained in this Annual Report on Form 10-K. This discussion contains forward looking statements and involves numerous risks and uncertainties, including, but not limited to, those described in the “Risk Factors” section of this Annual Report on Form 10-K. Actual results may differ materially from those contained in any forward-looking statements. For a discussion on forward-looking statements, see the information set forth in the introductory note to this Annual Report under the caption “Cautionary Note Regarding Forward Looking Statements,” which information is incorporated herein by reference. Unless the context otherwise requires, references to “we”, “us”, “our”, the “Company” or “Quantum-Si” are intended to mean the business and operations of Quantum-Si Incorporated and its consolidated subsidiaries. For discussion and analysis pertaining to the year ended December 31, 2024 overview and highlights as compared to the year ended December 31, 2023, please refer to the Company’s Annual Report on Form 10-K, as filed with the SEC on March 3, 2025.

Overview

We are a life sciences company focused on proteomics research, with the mission of transforming single-molecule analysis and democratizing its use by providing researchers and clinicians access to the proteome, the set of proteins expressed within a cell. We have developed a proprietary, universal, single-molecule detection platform that we are applying to proteomics to enable next-gen protein sequencing (“NGPS”) to sequence proteins in a massively parallel fashion (rather than sequentially, one at a time), which can also be used for the study of nucleic acids. We believe in the ability to sequence proteins in a massively parallel fashion and offer a fast analysis time provides NGPS with the potential to unlock significant biological information through improved resolution and unbiased access to the proteome at a speed and scale not available today. Traditionally, proteomic workflows to sequence proteins required days or weeks to complete. Our current platform includes our Platinum® NGPS line of instruments, Platinum Analysis Software and consumable kits for use with our Platinum line of instruments. In 2021, we introduced our Platinum early access program to sites with participation from leading academic centers and key industry partners. The early access program introduced the Platinum single-molecule sequencing system to key opinion leaders across the globe for both expansion and development of applications and workflows. We began a controlled launch of the Platinum instrument and started to take orders in December 2022, subsequently began a controlled commercial launch of Platinum in January 2023 and then moved to a full commercial launch of Platinum beginning in the second quarter of 2024. In January 2025, we announced the launch of our Platinum Pro benchtop sequencer. First shipments of Platinum Pro occurred in March 2025.

We believe our platform offers a differentiated solution in a rapidly evolving proteomics tools market. Within our initial focus market of proteomics, our platform is designed to provide users a seamless opportunity to gain key insights into the immediate state of biological pathways and cell state. Our platform aims to address many of the key challenges and bottlenecks with legacy proteomic solutions, such as mass spectrometry (“MS”), which include high instrument costs both in terms of acquisition and ownership, and complexity with data analysis, which together limit broad adoption. We believe our platform, which is designed to streamline sequencing and data analysis at a lower instrument cost and with greater automation than legacy proteomic solutions, could allow our product to have wide utility across the study of the proteome. For example, our platform could be used for biomarker discovery and disease detection, pathway analysis, immune response, vaccine development, quality assurance and quality control, among other applications.

In November 2025, we presented an updated technology and product roadmap that we believe positions us to be a leader in proteomics, including instrumentation, consumable kits and software tools. We intend to continue to execute on this roadmap through a combination of internal development programs and external partnerships to bring to market the most comprehensive proteomics platform in our industry.

Most importantly, this roadmap includes the development of ProteusTM, our next-generation platform, which was announced in November 2024 and is anticipated to launch by the end of 2026. Proteus aims to provide single-molecule, amino acid level resolution while also providing anticipated significantly higher sequencing output per sample and increased sample throughout per run, automation of the sequencing workflow and automated data analysis as compared to Platinum Pro. The Proteus platform is being developed to be a modular, scalable system that allows for expansion in the overall platform, the number of consumables that can be processed concurrently and the overall output of sample data from the platform. The first generation of Proteus and associated sequencing consumables is anticipated to include motion control, liquid handling, and a new on-board single optical system with the ability to accept a new consumable chip that has

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approximately 80 million features. We believe this new platform will provide much deeper insights while simplifying and significantly reducing the cost of the underlying consumable. In addition, during our presentation in November 2025, we provided data demonstrating the wide range of proteomics applications that are addressable with our proprietary, single-molecule, kinetic detection technology.

Global Developments

Although the U.S. Federal Reserve lowered interest rates slightly in 2024 and in the third and fourth quarters of 2025, it is not known whether additional action will be taken to lower interest rates and if this decrease, and any other decreases, will have an impact on inflation. While these rate fluctuations have not had a significant adverse impact on the Company to date, the impact of such rate fluctuations on the overall financial markets and the economy may adversely impact the Company in the future. In addition, the global economy has experienced and is continuing to experience high levels of inflation and global supply chain disruptions. The Company continues to monitor these supply chain, inflation and interest rate factors, as well as the uncertainty resulting from the overall economic environment.

To date, the Company has not been materially affected by enacted tariffs either by the U.S. government or foreign retaliatory tariffs; however, the Company’s finished goods and/or their components could become materially affected by changing tariffs in the future. If increased tariffs are imposed on the Company’s finished goods and/or components, they may impact the business, financial condition, results of operations and cash flows.

Although the Company has not been significantly impacted by geopolitical conflicts throughout the world, the Company has experienced certain constraints in product and material availability and increasing costs required to obtain certain materials and supplies as a result of these conflicts on the global economy. To date, the business has not been materially impacted by these conflicts, however, as the conflicts continue or worsen, they may impact the business, financial condition, results of operations and cash flows.

Restructuring

In November 2024, we announced that we committed to an organizational restructuring program designed to streamline and focus our overall corporate resources, as well as align required resources to focus on future product development objectives, including our recently announced Proteus platform. As a result, we terminated approximately 23% of our 187 employee workforce. In connection with the restructuring, we recognized one-time cash charges related to severance and other benefits of approximately $2.3 million in the fourth quarter of 2024. Our restructuring activities were complete as of December 31, 2024 and, as of December 31, 2025, we do not expect to incur additional charges associated with these activities. For further information regarding our restructuring activities, please refer to Note 13.Restructuringin the accompanying notes to the Consolidated Financial Statements included elsewhere in this Annual Report on Form 10-K.

Equity Transactions

At-the-Market Equity Offering Program

On September 26, 2025, we entered into a Sales Agreement (the “Sales Agreement”) with Leerink Partners LLC (“Leerink”), pursuant to which we may offer and sell shares of our Class A common stock having an aggregate offering price of up to $100.0 million, from time to time through an “at-the-market” offering program under which Leerink will act as sales agent (the “2025 ATM Offering”). We have no obligation to sell any shares under the Sales Agreement and may at any time suspend solicitation and offers under the Sales Agreement. The 2025 ATM Offering is being made pursuant to a universal shelf registration statement on Form S-3, which we originally filed on September 26, 2025, and a sales agreement prospectus related to the 2025 ATM Offering. During the year ended December 31, 2025, there were no shares sold under the Sales Agreement.

Registered Direct Offerings and Pre-funded Warrants

On July 3, 2025, we entered into a securities purchase agreement with a certain institutional investor, pursuant to which we agreed to issue and sell, in a registered direct offering (the “July 2025 Registered Direct Offering”), an aggregate of (i) 18,200,000 shares of our Class A common stock at a price of $1.67 per share and (ii) pre-funded warrants to purchase 11,740,119 shares of Class A common stock (the “Pre-Funded Warrants”). The Pre-Funded Warrants were exercised in full on August 1, 2025 at the exercise price of 0.0001 for one share of Class A common stock per Pre-Funded Warrant. The gross proceeds from the July 2025 Registered Direct Offering were $50.0 million. After deducting estimated placement

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agents’ fees and other offering expenses payable by us, net proceeds as of December 31, 2025 were approximately $46.7 million.

In addition, in connection with the July 2025 Registered Direct Offering, we provided written notice, effective as of July 3, 2025, to Canaccord Genuity LLC (“Canaccord”) of our election to terminate the equity distribution agreement dated December 11, 2024 for our at-the-market offering. At the time of termination, we had sold 23,425,650 shares of our Class A common stock under the equity distribution agreement for aggregate gross proceeds of $36.2 million.

On January 3, 2025, we entered into a securities purchase agreement with certain institutional investors pursuant to which we agreed to issue and sell, in a registered direct offering (the “January 2025 Registered Direct Offering,” and together with the July 2025 Registered Direct Offering, the “Registered Direct Offerings”) an aggregate of 15,625,000 shares of our Class A common stock at a price of $3.20 per share. The gross proceeds from the January 2025 Registered Direct Offering were $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by us, net proceeds recorded as of December 31, 2025 were approximately $46.8 million.

In connection with both Registered Direct Offerings, we entered into placement agency agreements with A.G.P./Alliance Global Partners (“AGP”), pursuant to which AGP agreed to serve as our sole placement agent on a reasonable best efforts basis. In connection with the Registered Direct Offerings, we agreed to pay AGP an aggregate cash fee equal to 6.0% of the gross proceeds received in the respective offering. The securities in both Registered Direct Offerings were sold pursuant to our universal shelf registration statement on Form S-3, which was originally filed with the SEC on August 11, 2023, and related base prospectuses and prospectus supplements dated July 3, 2025 and January 3, 2025, respectively, thereunder.

For further information regarding our equity transactions, please refer to the Liquidity Outlook section below.

Critical Accounting Policies and Significant Judgments and Estimates

Our management’s discussion and analysis of our financial condition and results of operations is based on our Consolidated Financial Statements, which have been prepared in accordance with U.S. GAAP. The preparation of these Consolidated Financial Statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the Consolidated Financial Statements, as well as expenses incurred during the reporting periods. Our estimates are based on historical experience and various other factors we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about items not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

Revenue Recognition

Revenue is derived from sales of products and services. Product revenue is primarily generated from the sales of instruments and consumables used in protein sequencing and analysis. Service revenue is primarily generated from service maintenance contracts including access to analysis software and advanced training for instrument use. We recognize revenue when or as a customer obtains control of the promised goods and services. The amount of revenue recognized reflects the consideration to which we expect to be entitled in exchange for these goods and services. This process involves identifying the contract with a customer, determining the performance obligations in the contract, determining the contract price, allocating the contract price to the distinct performance obligations in the contract, and recognizing revenue as the performance obligations have been satisfied. We have made the accounting policy election allowed for under ASC 606-10-32-2A to exclude all sales taxes from transaction price. Revenue recognition for contracts with multiple deliverables is based on the separate satisfaction of each distinct performance obligation within the contract. A performance obligation is considered distinct from other obligations in a contract when it provides a benefit to the customer either on its own or together with other resources that are readily available to the customer and is separately identified in the contract. We allocate transaction price to the performance obligations in a contract with a customer based on the relative standalone selling price of each performance obligation. We determine standalone selling price based on the price at which the performance obligation is sold separately. If the standalone selling price is not observable through past transactions, we estimate the standalone selling price taking into account available information and specific factors such as competitive positioning, internal costs, profit objectives, and internally approved pricing guidelines related to the performance obligation.

We consider performance obligation for sales of products satisfied upon shipment of the goods to the customer in accordance with the shipping terms (either upon shipment or delivery), which is when control of the product is deemed to

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be transferred; this includes instruments and consumables. Customers generally do not have a right to return products, except for defective or damaged products during the warranty period or unless prior written consent is provided. In instances where right of payment or transfer of title is contingent upon the customer’s acceptance of the product, revenue is deferred until all acceptance criteria have been met. Revenues for service maintenance contracts, which start after the first year of purchase and are considered as service type warranties that effectively extend the standard first-year service coverage at the customer’s option are recognized ratably over the contract service period as these services are performed evenly over time. Revenues for advanced training is recognized at a point in time upon satisfaction of the underlying performance obligation. We typically provide a standard one-year warranty which covers defects in materials, workmanship and manufacturing or performance conditions under normal use and service. The first year of the warranty of the products is considered an assurance-type warranty and is recorded as Cost of revenue within the Consolidated Statements of Operations and Comprehensive Loss. We have determined this standard first-year warranty is not a distinct performance obligation.

Stock-based Compensation

Stock-based compensation expense for stock option grants with only service conditions is recognized on a straight-line basis over the requisite service period of the individual grants, which is generally the vesting period, based on the estimated grant date fair values. Stock-based compensation expense for stock option grants subject to non-financing event performance conditions on an accelerated basis is recognized as though each vesting portion of the award was, in substance, a separate award.

Prior to the Business Combination, the fair value of the shares of common stock underlying stock options had been determined by the Board, with input from management and contemporaneous third-party valuations, as there was no public market for the common stock. Given the absence of a public trading market for our common stock, the Board exercised reasonable judgment and considered numerous objective and subjective factors to determine the best estimate of the fair value of our common stock at each option grant date.

After the completion of the Business Combination, we measure compensation expense for stock-based awards to employees, non-employees and directors based upon the awards’ initial grant-date fair values. Stock-based compensation expense for stock options, restricted stock units and performance awards is recorded over the requisite service period. For awards with only a service condition, we expense stock-based compensation using the straight-line method over the requisite service period for the entire award. For awards with a market condition, we expense the grant date fair value at the target over the vesting period regardless of the value the award recipients ultimately receive. The fair value of restricted stock without a market condition is estimated using the current market price of our common stock on the date of grant. The fair value of stock option grants with a market condition is estimated at the date of grant using the Monte Carlo simulation model (“Monte Carlo”). The fair values of stock option grants with only a service condition are estimated as of the date of grant by applying the Black-Scholes option valuation model (“Black-Scholes model”). The Black-Scholes model and Monte Carlo models incorporate assumptions as to stock price volatility, the expected life of options or restricted stock, a risk-free interest rate and dividend yield. The effect of forfeiture in compensation costs is recognized based on actual forfeitures when they occur.

The Black-Scholes model is affected by the stock price on the date of the grant as well as assumptions regarding a number of variables. These variables include the expected term of the option, expected risk-free interest rate, the expected volatility of common stock, and expected dividend yield; each of which is described below. The assumptions for expected term of the option and expected volatility of common stock are the two assumptions that significantly affect the grant date fair value.

•Expected Term: The expected term is calculated using the weighted-average period that the stock options are expected to be outstanding prior to being exercised. We determine expected term based on historical exercise patterns and our expectation of the time that it will take for employees to exercise options still outstanding. We estimate non-employees’ options based on the contractual term.

•Risk-free Interest Rate: The risk-free interest rate for periods within the expected term of the awards is based on the U.S. Treasury yield curve in effect at the time of the grant.

•Expected Stock Price Volatility: We determined expected annual equity volatility based on the combination of the historical volatility of our common stock and the historical volatility of the common stock comparable to our common stock.

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•Dividend Yield: Because we have never paid a dividend and do not expect to begin doing so in the foreseeable future, we assume no dividend yield in valuing the stock-based awards.

•Exercise Price: The exercise price is taken directly from the grant notice issued to employees and non-employees.

Stock options granted to non-employees are accounted for based on their fair value on the measurement date using the Black-Scholes model. For further information regarding our stock-based compensation and equity incentive plans, please refer to Note 2. Summary of Significant Accounting Policies and Note 10. Stock-based Compensation in the accompanying notes to our Consolidated Financial Statements included elsewhere in this Annual Report on Form 10-K.

Inventory

Inventory is stated at the lower of cost or net realizable value with cost determined using the first-in, first-out method. Materials that may be utilized for either commercial or, alternatively, for research and development purposes, are classified as inventory. Amounts in inventory used for research and development purposes are charged to research and development expense when the product enters the research and development process and can no longer be used for commercial purposes and, therefore, does not have an “alternative future use” as defined in authoritative guidance. During the years ended December 31, 2025, 2024 and 2023, we identified $1.6 million, $3.2 million and $3.4 million, respectively, of product that no longer had an alternative future use and therefore was included as part of research and development expense.

An assessment of the recoverability of capitalized inventory is performed during each reporting period and, if needed, we record a reserve for any excess and obsolete inventory to record inventory at its estimated net realizable value in the period it is identified. Inventory excess and obsolescence reserves related to cost of revenue were $0.7 million and $0.2 million for the years ended December 31, 2025 and 2024, respectively. Inventory excess and obsolescence reserves related to cost of revenue were immaterial for the year ended December 31, 2023.

For further information regarding our significant accounting policies and estimates, please refer to Note 2. Summary of Significant Accounting Policies in the accompanying notes to our Consolidated Financial Statements included elsewhere in this Annual Report on Form 10-K.

Warrant Liabilities

Outstanding warrants include Public Warrants which were issued as one-third of one redeemable warrant per unit during HighCape’s initial public offering on September 9, 2020, and Private Warrants sold to the Sponsor. The Public Warrants and Private Warrants meet the definition of a derivative and we recorded these warrants as warrant liabilities on the Consolidated Balance Sheets at fair value upon the closing of the Business Combination, with subsequent changes in their respective fair values recognized in the Consolidated Statements of Operations and Comprehensive Loss at each reporting date. Both the Public Warrants and Private Warrants expire on June 10, 2026. For further information regarding our warrants, please refer to Note 11. Warrant Liabilities in the accompanying notes to the Consolidated Financial Statements included elsewhere in this Annual Report on Form 10-K.

Recently Issued Accounting Pronouncements

For a discussion of recently adopted accounting pronouncements and accounting pronouncements pending adoption, please refer to Note 2. Summary of Significant Accounting Policies in the accompanying notes to the Consolidated Financial Statements included elsewhere in this Annual Report on Form 10-K.

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Results of Operations for the Year Ended December 31, 2025 as Compared to the Year Ended December 31, 2024

The following table summarizes the results of our operations for the years ended December 31, 2025 and 2024 (dollars in thousands):

Revenue

Cost of revenue

Operating expenses:

Legal settlement expense, net of insurance proceeds 5,162 — 5,162 nm(1)

Provision for income taxes (58) (56) (2) 3.6 %

(1) “nm” indicates change is not meaningful.

Revenue, Cost of Revenue and Gross Profit

Revenue is derived from sales of products and services. Product revenue is generated from the following sources: (i) sales of our Platinum line of instruments, (ii) consumables kits, including Library Preparation Kits, Sequencing Kit (which includes sequencing reagents and semiconductor chips), and other related reagent kits, and (iii) freight revenue, which is recognized upon shipment. Service revenue is generated from service maintenance contracts including Platinum Analysis Software access, and advanced training for instrument use.

Cost of revenue primarily consists of product and service costs including material costs, personnel costs and benefits, inbound and outbound freight, packaging, warranty replacement costs, royalty costs, facilities costs, depreciation and amortization expense, and inventory write-offs.

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Revenue, Cost of revenue and Gross profit for the years ended December 31, 2025 and 2024 are as follows (dollars in thousands):

Revenue

Cost of revenue

Gross profit margin 47.3 % 52.3 %

Total revenue for the sale of our Platinum line of instruments, related reagent kits and service maintenance contracts decreased by $0.6 million, or 20.3% for the year ended December 31, 2025 as compared to the same period in 2024. During the year ended December 31, 2025, we experienced longer capital sales cycles, largely driven by low or no capital spend budgets at certain customers, primarily from actual and potential budget cuts from the National Institute of Health (“NIH”).

Total cost of revenue decreased $0.2 million, or 12.0%, for the year ended December 31, 2025 as compared to the same period in 2024. The change in the cost of revenue is based on the relative volume and revenue decreases for the year ended December 31, 2025 as compared to the prior year.

Gross profit decreased $0.4 million, or 27.9% for the year ended December 31, 2025 as compared to the same period in 2024.

Gross profit margin was 47.3% for the year ended December 31, 2025 as compared to 52.3% for the same period in 2024. This change in margin was primarily based on the mix of products sold during each period and the inventory utilization impacted by purchase price variance and other valuation adjustments for items carried at low or no value that predates the commercial launch of our Platinum line of instruments. We expect gross profit margin to fluctuate for the foreseeable future as we work through our continued commercialization efforts.

We began a controlled launch of the Platinum instrument and started to take orders in December 2022, and subsequently began a controlled commercial launch of Platinum in January 2023, and then moved to a full commercial launch of Platinum beginning in the second quarter of 2024. In January 2025, we announced the launch of our Platinum Pro benchtop sequencer. First shipments of Platinum Pro occurred in March 2025.

Research and Development Expenses

Research and development expenses primarily consist of personnel costs and benefits, stock-based compensation, lab supplies, consulting and professional services, fabrication services, charges related to product without an alternative future use, facilities costs, software, and other outsourced expenses. Research and development expenses are recognized as incurred. Our research and development expenses are primarily related to developing new products and services.

Research and development expenses for the years ended December 31, 2025 and 2024 are as follows (dollars in thousands):

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Research and development expenses decreased by $5.9 million, or 9.9%, for the year ended December 31, 2025 as compared to the same period in 2024. This decrease was primarily driven by a $3.6 million decrease in payroll, payroll-related and other personnel costs resulting primarily from the reduction in headcount related to the November 2024 restructuring, a $2.4 million decrease in research and development expenses due to refundable tax credits, a $2.0 million decrease in laboratory supplies expense, a $0.9 million net decrease in excess and obsolete inventory with no alternative future use and a $0.4 million decrease in consulting expense. These decreases were partially offset by a $3.8 million increase in fabrication and outsourced services driven by efforts to support the development of our Proteus platform.

Selling, General and Administrative Expenses

Selling, general and administrative expenses primarily consist of personnel costs and benefits, stock-based compensation, patent and filing fees, consulting and professional services, legal and accounting services, facilities costs, depreciation and amortization expense, insurance and office expenses, product advertising and marketing.

Selling, general and administrative expenses for the years ended December 31, 2025 and 2024 are as follows (dollars in thousands):

Selling, general and administrative expenses decreased by $5.8 million, or 11.4%, for the year ended December 31, 2025 as compared to the same period in 2024. This decrease was primarily due to a $2.9 million decrease in legal fees, a $2.1 million decrease in payroll, payroll-related and other personnel costs, a $0.6 million decrease in non-income tax expense, a $0.5 million decrease in depreciation expense, a $0.5 million decrease in insurance expense due to lower premiums and a $0.9 million net decrease in other expenses. These decreases were partially offset by a $1.7 million increase in stock-based compensation expense.

Lease Termination Expense, Net

For the years ended December 31, 2025 and 2024, Lease termination expense, net, is as follows (dollars in thousands):

Lease termination expense, net $ 13,577 $ — $ 13,577 nm(1)

(1) “nm” indicates change is not meaningful.

Lease termination expense, net, increased $13.6 million for the year ended December 31, 2025, when compared to the same period in 2024. This increase was due to a settlement agreement to terminate the New Haven, Connecticut lease. For further details regarding this settlement, please refer to Note 17. Commitments and Contingenciesin the accompanying notes to the Consolidated Financial Statements included elsewhere in this Annual Report on Form 10-K.

Legal Settlement Expense, Net of Proceeds

For the years ended December 31, 2025 and 2024, Legal settlement expense, net of proceeds, is as follows (dollars in thousands):

Legal settlement expense, net of insurance proceeds $ 5,162 $ — $ 5,162 nm(1)

(1) “nm” indicates change is not meaningful.

Legal settlement expense, net of insurance proceeds, increased $5.2 million for the year ended December 31, 2025, as compared to the same period in 2024. This increase was due to a $3.4 million preliminary legal settlement being reached for the Delaware Stockholder Litigation in the second quarter of 2025 and a $1.8 million settlement being paid to the prior contract manufacturer that had manufactured the Platinum and Carbon instruments in the third quarter of 2025. For further

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information on these settlements, please refer to Note 17. Commitments and Contingenciesin the accompanying notes to the Consolidated Financial Statements included elsewhere in this Annual Report on Form 10-K.

Dividend Income and Interest Income

For the year ended December 31, 2025 and 2024, dividend income and interest income are derived primarily from fixed income securities and money market mutual funds, respectively.

Dividend income and interest income for the years ended December 31, 2025 and 2024 is as follows (dollars in thousands):

Dividend income and interest income decreased by $1.0 million and $0.7 million, respectively, or 59.7% and 7.0%, respectively, for the year ended December 31, 2025 as compared to the same period in 2024. These decreases are a result of lower market interest rates on invested capital as well as relative lower invested balances during the year ended December 31, 2025.

Change in Fair Value of Warrant Liabilities

The warrant liabilities were recorded at fair value as part of the Business Combination. Change in fair value of warrant liabilities primarily consists of the change in the fair value of our Public Warrants and Private Warrants.

Change in warrant liabilities for the years ended December 31, 2025 and 2024 is as follows (dollars in thousands):

For the year ended December 31, 2025 we recognized $4.2 million of income from the decrease in the fair value of warrant liabilities as compared to $3.7 million of expense from the increase in fair value of warrant liabilities for the same period in 2024. These changes in the fair value of warrant liabilities were primarily driven by the change in the underlying trading price of our Class A common stock during the periods reported.

Other Expense, Net

Other expense, net, typically consists of currency revaluations and income from credit card cash rewards programs. Other expense, net, for the years ended December 31, 2025 and 2024 is as follows (dollars in thousands):

Other (expense) income, net, increased by $1.0 million, or 5126.3%, for the year ended December 31, 2025 as compared to the same period in 2024. In addition to the items mentioned above, the year ended December 31, 2025 also includes a legal settlement payment received of $1.0 million.

Liquidity and Capital Resources

The following table presents a summary of our consolidated cash flows for operating, investing, and financing activities for the years ended December 31, 2025 and 2024 (in thousands):

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Net cash (used in) provided by:

Net cash used in operating activities $ (94,717) $ (87,795)

Net cash used in investing activities (28,320) (32,675)

Net cash provided by financing activities 95,423 35,876

Effect of exchange rate changes on cash and cash equivalents 12 (25)

Net decrease in cash and cash equivalents $ (27,602) $ (84,619)

Net cash used in operating activities

For the year ended December 31, 2025, net cash used in operating activities of $94.7 million was primarily due to a net loss of $101.3 million, resulting from continued spend on research and development and commercialization efforts, accretion on marketable securities of $8.0 million, net changes in operating assets and liabilities of $4.6 million and a change in fair value of warrant liabilities of $4.2 million, which was primarily driven by the change in the underlying trading price of our Class A common stock. This cash used in operating activities was partially offset by stock-based compensation of $10.8 million, depreciation and amortization of $4.5 million, a loss on lease termination of $2.3 million related to the New Haven, Connecticut lease, non-cash lease expense of $2.3 million, write-downs of inventory of $2.3 million and a $1.2 million write-off of construction in process related to the termination of the New Haven, Connecticut lease.

For the year ended December 31, 2024, net cash used in operating activities of $87.8 million was primarily due to a net loss of $101.0 million resulting from continued spend on research and development and commercialization efforts, accretion on marketable securities of $8.4 million and a $3.2 million write-down of inventory. This cash used in operating activities was partially offset by stock-based compensation of $8.9 million, a net increase in cash provided by operating assets and liabilities of $4.6 million due to timing of cash receipts and disbursements, depreciation and amortization of $4.6 million, a change in fair value of warrant liabilities of $3.7 million, and non-cash lease expense of $2.4 million.

Net cash used in investing activities

For the year ended December 31, 2025, net cash used in investing activities was $28.3 million as compared to $32.7 million for the same period in 2024. This decrease in cash used was primarily due to a $37.4 million increase in cash provided by proceeds from the sales and maturities of marketable securities and a $2.1 million decrease in purchases of property and equipment partially offset by a $35.1 million increase in cash used for purchases of marketable securities.

Net cash provided by financing activities

For the year ended December 31, 2025, net cash provided by financing activities was $95.4 million as compared to $35.9 million for the same period in 2024. This increase in cash provided was primarily due to $93.5 million of net proceeds from the issuance of common stock from net direct equity and pre-funded warrant offerings that occurred in January and July of 2025 and $1.9 million in proceeds from the exercise of stock options. Further information regarding the direct equity and pre-funded warrant offerings can be found below under the header Liquidity Outlook.

Liquidity Outlook

Since our inception, we have funded our operations primarily with proceeds from the issuance of equity to private investors, as well as with the proceeds received from the closing of the Business Combination. Additionally, we began to generate revenue during 2023 from commercial sales of our Platinum instrument. Our primary uses of liquidity have been operating expenses, capital expenditures and our acquisition of certain assets. Cash flows from operations have been historically negative as we continue to invest in the development of our technology in NGPS. Going forward, we anticipate debt or equity offerings will be the primary source of funds to support our operating needs and capital expenditures until we reach scale of our commercial operations. We expect to incur negative operating cash flows on an annual basis for the foreseeable future until such time that we can scale our revenue growth.

We expect our existing cash and cash equivalents and investments in marketable securities, together with revenue from the sale of our products and services, will be sufficient to meet our liquidity, capital expenditure, and anticipated working capital requirements and fund our operations for at least the next 12 months. We expect to use our cash and cash equivalents and investments in marketable securities and funds from revenue generated to invest in our continued

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commercialization efforts, to further invest in research and development, for other operating expenses, business acquisitions and for working capital and general corporate purposes.

As of December 31, 2025, we had cash and cash equivalents and investments in marketable securities totaling $215.8 million. Our future capital requirements may vary from those currently planned and will depend on various factors including the pace and success of product commercialization.

Our ongoing commercialization of Platinum and Platinum Pro as well as our continuing research and development efforts to enhance our instruments may require an accelerated amount of spending to enhance the sales and marketing teams, continue to drive development, and build inventory. Other factors that could accelerate cash needs include: (i) delays in achieving scientific and technical milestones, (ii) unforeseen capital expenditures and fabrication costs related to manufacturing for commercialization, (iii) changes we may make in our business or commercialization strategy, (iv) costs of running a public company, (v) other items affecting our forecasted level of expenditures and use of cash resources, including potential acquisitions, and (vi) increased product and service costs.

On August 11, 2023, we filed a universal shelf registration statement on Form S-3 (the “2023 Shelf Registration Statement”) covering the offering of Class A common stock, preferred stock, debt securities, warrants, rights and units. After the closing of the July 2025 Registered Direct Offering, the remaining capacity of the 2023 Shelf Registration Statement was approximately $13.8 million. We filed a universal shelf registration statement on Form S-3 and a subsequent amendment to the Form S-3 (the “2025 Shelf Registration Statement”), on September 26, 2025 and October 9, 2025, respectively, covering the offering of Class A common stock, preferred stock, debt securities, warrants, rights and units.

On December 11, 2024, we entered into an Equity Distribution Agreement (the “Canaccord Sales Agreement”) with Canaccord to sell shares of our Class A common stock having an aggregate offering price of up to $75.0 million, from time to time through an “at-the-market” offering program under which Canaccord acted as sales agent (the “2024 ATM Offering”). We had no obligation to sell any shares under the Canaccord Sales Agreement and could at any time suspend solicitation and offers under the Canaccord Sales Agreement. The 2024 ATM Offering was made pursuant to the 2023 Shelf Registration Statement and a prospectus supplement related to the 2024 ATM Offering dated December 11, 2024. During the year ended December 31, 2024, we sold and issued 23,425,650 shares of our Class A common stock under the 2024 ATM Offering, resulting in gross proceeds of $36.2 million. Net proceeds were $34.8 million after commissions and issuance costs of $1.4 million. We sold no shares of our Class A common stock under the 2024 ATM Offering during the year ended December 31, 2025. In connection with the July 2025 Registered Direct Offering, we provided written notice, effective as of July 3, 2025, to Canaccord of our election to terminate the Canaccord Sales Agreement for our at-the-market offering. At the time of termination, we had sold 23,425,650 shares of our Class A common stock under the Canaccord Sales Agreement for aggregate gross proceeds of $36.2 million.

On January 3, 2025, we entered into a securities purchase agreement with certain institutional investors in connection with the January 2025 Registered Direct Offering. The gross proceeds from the January 2025 Registered Direct Offering were $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by us, net proceeds recorded as of December 31, 2025 were approximately $46.8 million.

On July 3, 2025, we entered into a securities purchase agreement with a certain institutional investor in connection with the July 2025 Registered Direct Offering. The Pre-Funded Warrants were exercised in full on August 1, 2025 at the exercise price of $0.0001 for one share of Class A common stock per Pre-Funded Warrant. The gross proceeds from the July 2025 Registered Direct Offering were $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by us, net proceeds as of December 31, 2025 were approximately $46.7 million.

On September 26, 2025, we entered into the Leerink Sales Agreement. We have no obligation to sell any shares under the Leerink Sales Agreement and may at any time suspend solicitation and offers under the Leerink Sales Agreement. The 2025 ATM Offering is being made pursuant to the 2025 Shelf Registration Statement and a prospectus supplement related to the 2025 ATM Offering. During the year ended December 31, 2025, there were no shares sold under the Leerink Sales Agreement. Shares offered and sold in the 2025 ATM Offering, if any, will be sold pursuant to the 2025 Shelf Registration Statement.

In the future, we may be unable to obtain any required additional financing on terms favorable to us, if at all. If adequate funds are not available to us on acceptable terms or otherwise, we may be unable to successfully develop or enhance products and services, respond to competitive pressure or take advantage of acquisition opportunities, any of which could have a material adverse effect on our business, financial condition, operating results and cash flows.

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Related Party Transactions

For a description of our related party transactions, please refer to Note 16. Related Party Transactions in the accompanying notes to the Consolidated Financial Statements included elsewhere in the Annual Report on Form 10-K.

Capital Expenditures

During the year ended December 31, 2025, capital expenditures were $2.5 million. We forecast capital expenditures in order to execute on our business plan and maintain growth; however, the actual amount and timing of such capital expenditures will ultimately be determined by the volume of business. We currently anticipate our capital expenditures for the year ended December 31, 2026 will be approximately $5.0 million. We have funded and plan to continue funding these capital expenditures with cash and financing.

Contractual Obligations

Leases

We lease certain facilities and equipment under noncancellable lease agreements that expire at various dates through 2029. As of December 31, 2025, the future lease payments, before adjustments for tenant incentives, were approximately $4.6 million.

Licenses related to certain intellectual property

We license certain intellectual property, some of which may be utilized in our current or future product offerings. To preserve the right to use such intellectual property, we are required to make annual minimum fixed payments totaling approximately $0.2 million as well as royalties based on net sales if the royalties exceed annual minimum fixed payments.

Item 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Inflation risk

We believe inflation can and has had an impact on the underlying cost of our supplies and manufacturing components related to our business. To the extent our costs are impacted by general inflationary pressures, we may not be able to fully offset such higher costs through price increases or manufacturing efficiencies. Our inability or failure to do so could harm our business, financial condition, results of operations or cash flows.

Interest rate risk

As of December 31, 2025, our marketable securities are comprised primarily of investments in money market funds backed by U.S. government issued securities, U.S. Treasury bills, and high-quality corporate commercial paper. The primary objective of our investments is the preservation of capital to fulfill liquidity needs. We do not enter into investments for trading or speculative purposes. Based on the nature of our holdings, future interest rate changes are not expected to have a material impact on our marketable securities.

Foreign currency risk

Presently, we operate our business primarily within the United States, with limited sales outside the United States. To date, we have executed the majority of our transactions in U.S. dollars. In the future, we anticipate expanding into Europe and other locations outside the United States. This expansion may include transacting business in currencies other than the U.S. Dollar. Despite this, we anticipate conducting limited activity outside the U.S. Dollar in the near term, and therefore foreign currency translation risk is not expected to have a material impact on our Consolidated Financial Statements. However, the growth of our operations, scope of transactions outside the United States, and the use of currencies other than the U.S. Dollar may grow in the future, at which point it is possible foreign currency translation will have a material effect on our operations. To date, we have not entered into any hedging arrangements with respect to foreign currency risk. As our international operations grow, we will continue to reassess our approach to managing our risk relating to fluctuations in currency rates.

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ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

INDEX TO CONSOLIDATED FINANCIAL STATEMENTS

Consolidated Balance Sheets as of December 31, 2025 and 2024 82

Notes to the Consolidated Financial Statements 86

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Report of Independent Registered Public Accounting Firm

To the Board of Directors and Stockholders of Quantum-Si Incorporated

Opinion on the Financial Statements

We have audited the accompanying consolidated balance sheets of Quantum-Si Incorporated and its subsidiaries (the “Company”) as of December 31, 2025 and 2024, and the related consolidated statements of operations and comprehensive loss, of changes in stockholders’ equity (deficit) and of cash flows for the years then ended, including the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company as of December 31, 2025 and 2024, and the results of its operations and its cash flows for the years then ended in conformity with accounting principles generally accepted in the United States of America.

Basis for Opinion

These consolidated financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on the Company’s consolidated financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audits of these consolidated financial statements in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud. The Company is not required to have, nor were we engaged to perform, an audit of its internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Company’s internal control over financial reporting. Accordingly, we express no such opinion.

Our audits included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the consolidated financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements. We believe that our audits provide a reasonable basis for our opinion.

Critical Audit Matters

The critical audit matter communicated below is a matter arising from the current period audit of the consolidated financial statements that was communicated or required to be communicated to the audit committee and that (i) relates to accounts or disclosures that are material to the consolidated financial statements and (ii) involved our especially challenging, subjective, or complex judgments. The communication of critical audit matters does not alter in any way our opinion on the consolidated financial statements, taken as a whole, and we are not, by communicating the critical audit matter below, providing a separate opinion on the critical audit matter or on the accounts or disclosures to which it relates.

Lease Termination - Winchester

As described in Note 17 to the consolidated financial statements, in December 2021, the Company signed a 10-year lease with Winchester Office LLC (“Winchester”) as landlord. The lease commenced on January 8, 2022 with an original lease expiration date of July 31, 2032. On September 13, 2022, the Company filed a lawsuit against Winchester, alleging that Winchester had (i) refused to reimburse the Company for costs related to improvements already incurred and submitted, (ii) delayed the Company’s completion of improvements, in order to avoid reimbursing the costs of those improvements, and (iii) improperly rejected the Company’s proposed improvement plans. On September 23, 2025, the Company and Winchester entered into the mutual release agreement in connection with the lease. For the year ended December 31, 2025,

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the Company recorded $13.6 million of total lease termination expense, net, in consideration for Winchester’s agreement to terminate the lease as of the early termination date and settle all disputes between the parties.

The principal considerations for our determination that performing procedures relating to the lease termination - Winchester is a critical audit matter are a high degree of auditor effort in performing procedures and evaluating audit evidence related to the Company’s accounting for the lease termination.

Addressing the matter involved performing procedures and evaluating audit evidence in connection with forming our overall opinion on the consolidated financial statements. These procedures included, among others (i) obtaining and evaluating the lease and mutual release agreements; (ii) evaluating management’s assessment of the accounting treatment relating to the derecognition and settlement under the lease and mutual release agreements; (iii) confirming with internal and external counsel the extent to which the settlement is reasonably estimable; and (iv) evaluating the sufficiency of the Company’s disclosures in the consolidated financial statements.

/s/ PricewaterhouseCoopers LLP

San Diego, California

March 3, 2026

We have served as the Company’s auditor since 2024.

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REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

To the stockholders and the Board of Directors of Quantum-Si Incorporated:

Opinion on the Financial Statements

We have audited the accompanying consolidated statements of operations and comprehensive loss, changes in stockholders’ equity (deficit), and cash flows for the period ended December 31, 2023, and the related notes (collectively referred to as the “financial statements”) of Quantum-Si Incorporated and subsidiaries (the “Company”). In our opinion, the financial statements present fairly, in all material respects, the results of the Company’s operations and its cash flows for the period ended December 31, 2023, in conformity with accounting principles generally accepted in the United States of America.

Basis for Opinion

These financial statements are the responsibility of the Company’s management. Our responsibility is to express an opinion on the Company's financial statements based on our audit. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.

We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Company is not required to have, nor were we engaged to perform, an audit of its internal control over financial reporting. As part of our audit, we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Company’s internal control over financial reporting. Accordingly, we express no such opinion.

Our audit included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audit also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audit provides a reasonable basis for our opinion.

/s/ Deloitte & Touche LLP

New York, New York

February 29, 2024 (March 3, 2025, as to the effects of the adoption of ASU No. 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures)

We began serving as the Company’s auditor in 2020. In 2024 we became the predecessor auditor.

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QUANTUM-SI INCORPORATED

CONSOLIDATED BALANCE SHEETS

(in thousands, except share and par value amounts)

Assets

Current assets:

Accounts receivable, net of allowance of $270 and $124, respectively 561 1,333

Legal settlement insurance receivable 4,638 —

Prepaid expenses and other current assets 4,554 3,006

Marketable securities, non-current 52,855 —

Operating lease right-of-use assets 3,464 13,061

Liabilities and Stockholders’ Equity

Current liabilities:

Accrued payroll and payroll-related costs 5,903 5,331

Accrued legal settlement liability 8,000 —

Accrued expenses and other current liabilities 1,505 4,848

Warrant liabilities, current 794 —

Current portion of operating lease liabilities 1,844 3,698

Warrant liabilities, non-current — 4,995

Other long-term liabilities 34 19

Commitments and contingencies (Note 17)

Stockholders’ equity:

Accumulated other comprehensive (loss) income (6) 45

Total liabilities and stockholders’ equity $ 245,607 $ 247,871

The accompanying notes are an integral part of these Consolidated Financial Statements.

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QUANTUM-SI INCORPORATED

CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS

(in thousands, except per share amounts)

Years Ended December 31,

Revenue

Cost of revenue

Operating expenses:

Lease termination expense, net 13,577 — —

Legal settlement expense, net of insurance proceeds 5,162 — —

Unrealized gain on trading securities — — 10,690

Realized loss on trading securities — — (5,103)

Change in fair value of warrant liabilities 4,202 (3,722) (278)

Provision for income taxes (58) (56) —

Other comprehensive gain (loss):

Net unrealized (loss) gain on marketable securities, net of tax $ (63) $ 70 $ —

Foreign currency translation adjustment 12 (25) —

Total other comprehensive (loss) gain, net of tax (51) 45 —

The accompanying notes are an integral part of these Consolidated Financial Statements.

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QUANTUM-SI INCORPORATED

CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS’ EQUITY (DEFICIT)

(in thousands, except share amounts)

Shares Amount Shares Amount

Common stock issued upon exercise of stock options 1,825,660 — — — 357 — — 357

Stock-based compensation — — — — 8,516 — — 8,516

Common stock issued upon exercise of stock options 598,689 1 — — 1,071 — — 1,072

Stock-based compensation — — — — 8,887 — — 8,887

Net unrealized gain on marketable securities, net of tax — — — — — 70 — 70

Refund of issuance costs — — — — 14 — — 14

Foreign currency translation — — — — — (25) — (25)

Common stock issued upon exercise of stock options 830,228 — — — 1,912 — — 1,912

Net unrealized loss on marketable securities, net of tax — — — — — (63) — (63)

Foreign currency translation — — — — — 12 — 12

The accompanying notes are an integral part of these Consolidated Financial Statements.

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QUANTUM-SI INCORPORATED

CONSOLIDATED STATEMENTS OF CASH FLOWS

(in thousands)

Years Ended December 31,

Cash flows from operating activities:

Adjustments to reconcile net loss to net cash used in operating activities:

Allowance for credit losses 146 124 —

Loss on lease termination 2,260 — —

Write-off of construction on process due to lease termination 1,162 — —

Unrealized gain on trading securities, net — — (10,690)

Realized loss on trading securities, net — — 5,103

Accretion on marketable securities (8,022) (8,405) —

Loss on disposal of fixed assets 31 425 136

Change in fair value of warrant liabilities (4,202) 3,721 278

Change in fair value of contingent consideration — — (400)

Changes in operating assets and liabilities:

Legal settlement insurance receivable (4,638) — —

Prepaid expenses and other current assets (1,563) 486 2,159

Operating lease right-of-use assets — — (83)

Accrued expenses and other current liabilities (1,495) 4,021 (1,835)

Accrued legal settlement liability 8,000 — —

Other long-term liabilities 14 7 7

Cash flows from investing activities:

Internally developed software - capitalized costs — (59) (763)

Cash flows from financing activities:

Proceeds from vesting of restricted stock 1 1 —

Deferred offering costs — — (208)

Refund of issuance costs — 14 —

Effect of exchange rate changes on cash and cash equivalents 12 (25) —

Net (decrease) increase in cash and cash equivalents (27,602) (84,619) 49,541

Supplemental disclosure of cash flow information:

Cash paid for taxes $ 24 $ — $ —

Supplemental disclosure of non-cash investing and financing activities:

Property and equipment purchased but not paid $ 217 $ 337 $ 302

Transfers from inventory to property and equipment $ 1,029 $ — $ —

Deferred offering costs payable $ — $ 553 $ 105

The accompanying notes are an integral part of these Consolidated Financial Statements.

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QUANTUM-SI INCORPORATED

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

Note 1. Description of Business and Basis of Presentation

Background

Quantum-Si Incorporated (including its subsidiaries, “Quantum-Si”, “QSI”, or the “Company”) was incorporated in Delaware on June 10, 2020 as HighCape Capital Acquisition Corp. (“HighCape”). The Company’s legal name became Quantum-Si Incorporated following a business combination on June 10, 2021 between the Company and Q-SI Operations Inc. (formerly Quantum-Si Incorporated) (the “Business Combination”), which was founded in 2013.

Quantum-Si is a life sciences company focused on proteomics research, with the mission of transforming single-molecule analysis and democratizing its use by providing researchers and clinicians access to the proteome, the set of proteins expressed within a cell. The Company has developed a proprietary, universal, single-molecule detection platform that is applied to proteomics to enable next-gen protein sequencing (“NGPS”) to sequence proteins in a massively parallel fashion (rather than sequentially, one at a time), which can also be used for the study of nucleic acids. The Company believes in the ability to sequence proteins in a massively parallel fashion and offer a fast analysis time provides NGPS with the potential to unlock significant biological information through improved resolution and unbiased access to the proteome at a speed and scale not available today. Traditionally, proteomic workflows to sequence proteins required days or weeks to complete. The current platform includes the Platinum® NGPS line of instruments, Platinum Analysis Software and consumable kits for use with the Platinum line of instruments. In 2021, the Company introduced the Platinum early access program to sites with participation from leading academic centers and key industry partners. The early access program introduced the Platinum single-molecule sequencing system to key opinion leaders across the globe for both expansion and development of applications and workflows. The Company began a controlled launch of the Platinum instrument and started to take orders in December 2022, subsequently began a controlled commercial launch of Platinum in January 2023 and then moved to a full commercial launch of Platinum beginning in the second quarter of 2024. In January 2025, the Company announced the launch of the Platinum Pro benchtop sequencer. First shipments of Platinum Pro occurred in March 2025.

Liquidity and Capital Resources

The Company has historically financed its operations primarily with proceeds from the issuance of equity to private investors, as well as with the proceeds received from the closing of the Business Combination. The Company has incurred significant losses and negative cash flows from operations in all periods since inception and had an accumulated deficit of $698.0 million as of December 31, 2025. The Company has incurred significant operating losses, including net losses of $101.3 million, $101.0 million and $96.0 million for the years ended December 31, 2025, 2024 and 2023, respectively. As of December 31, 2025, the Company had cash, cash equivalents and investments in marketable securities of $215.8 million. Management believes the Company’s current cash, cash equivalents and marketable securities, together with revenue from the sales of its products and services, will be sufficient to fund its planned operations for at least the next twelve months from the date of the issuance of the accompanying Consolidated Financial Statements.

Until such time as the Company can generate significant revenue from product sales, if ever, it expects to finance its operations through private and public equity offerings, debt financings, and/or potential future collaboration, license and development agreements. However, there can be no assurance the Company will be able to complete any such transactions on acceptable terms or otherwise, and the Company may be unable to obtain sufficient additional capital when needed. The inability to raise capital as and when needed would have a negative impact on the Company’s financial condition and its ability to pursue its business strategy. The Company will need to generate significant revenue to achieve profitability and it may never do so.

Global Developments

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Basis of Presentation and Principles of Consolidation

The accompanying Consolidated Financial Statements include the accounts of the Company and have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) and pursuant to the accounting disclosure rules and regulations of the Securities and Exchange Commission (the “SEC”).All intercompany transactions are eliminated.

Reclassifications

Certain prior year amounts have been reclassified for consistency with the current year’s presentation.

Note 2. Summary of Significant Accounting Policies

Use of Estimates

The preparation of the Consolidated Financial Statements in conformity with U.S. GAAP requires the Company to make estimates and assumptions about future events that affect the amounts recorded in its Consolidated Financial Statements and accompanying notes. Future events and their effects cannot be determined with certainty. On an ongoing basis, management evaluates these estimates and assumptions. Significant estimates and assumptions include:

•inventory valuation;

•assumptions used for leases;

•valuation of warrant liabilities;

•valuation allowances with respect to deferred tax assets;

•assumptions associated with revenue recognition; and

•assumptions underlying the fair value used in the calculation of stock-based compensation.

The Company bases these estimates on historical and anticipated results and trends and on various other assumptions the Company believes are reasonable under the circumstances, including assumptions as to future events. Changes in estimates are recorded in the period in which they become known. Actual results could differ from those estimates, and any such differences may be material to the Consolidated Financial Statements.

Concentration of Business Risk

Financial instruments that potentially subject the Company to concentration of credit risk consist principally of cash and cash equivalents and marketable securities. As of December 31, 2025 and 2024, the Company’s marketable securities consist of mutual funds, U.S. Treasury securities, U.S. government agency bonds and commercial paper. For further information regarding marketable securities, please refer to Note 3. Investments in Marketable Securities. The Company also maintains balances in certain operating accounts above federally insured limits and, as a result, the Company is exposed to credit risk in the event of default by the financial institutions to the extent account balances exceed the amount insured by the Federal Deposit Insurance Corporation.

The Company sources certain key materials and components utilized in the Company’s products from single or limited suppliers. Historically, the Company has not experienced significant issues sourcing these materials and components. However, if these suppliers were not able to supply the requested amount of materials or components, it could take a

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considerable length of time to obtain alternative sources, which could affect the Company’s development efforts and commercial operations.

Segment Reporting

The Company’s Chief Operating Decision Maker (the “CODM”), its Chief Executive Officer, reviews financial information presented on a consolidated basis for purposes of assessing financial performance, making operating decisions and allocating resources. Accordingly, the Company has determined that it operates as a single reportable segment. For further discussion related to segment reporting, please refer to Note 15. Segment Information.

Foreign Currency Translation and Transactions

For the Company’s international operations, the local currency has been determined to be the functional currency. The results of its non-U.S. dollar-based operations are translated to U.S. dollars at the average exchange rates during the period. Assets and liabilities are translated at the rate of exchange prevailing on the balance sheet date. Equity is translated at the prevailing rate of exchange at the date of the equity transaction. The translational effects of revaluing non-functional currency assets and liabilities were immaterial for the years ended December 31, 2025, 2024 and 2023.

The Company realizes foreign currency gains/(losses) in the normal course of business based on movement in the applicable exchange rates. As of December 31, 2025 and 2024 and for the years ended December 31, 2025, 2024 and 2023, the effect of foreign currency translation and transactions on the Company’s Consolidated Financial Statements was immaterial.

Cash and Cash Equivalents

All highly liquid investments purchased with a maturity of three months or less are classified as cash equivalents. As of December 31, 2025 and 2024, cash and cash equivalents consist of a mix of cash and short-term money market accounts, U.S. Treasury securities, U.S. government agency bonds and commercial paper.

Accounts Receivable, Net

Accounts receivable, net, is stated at the amount the Company expects to collect from customers based on their outstanding invoices. The Company reviews accounts receivable regularly to determine if any receivable may not be collectible. Such accounts receivable have been reduced by an allowance for doubtful accounts, which is our best estimate of the amount of probable credit losses in our existing accounts receivable. The Company estimates the amount of the allowance for doubtful accounts necessary to reduce accounts receivable to its estimated net realizable value by analyzing the status of significant past due receivables and current and historical bad debt trends. The Company writes off accounts receivable against the allowance when it determines a balance is uncollectible and ceases collection efforts. As of December 31, 2025 and 2024, the Company recorded an allowance against accounts receivable of $0.3 million and $0.1 million, respectively. The Company did not write off any accounts receivable balances during the years ended December 31, 2025, 2024 and 2023.

Marketable Securities

The Company’s investments in marketable securities with original maturities of greater than three months and remaining maturities of less than one year are classified as Marketable securities, current, and investments with maturities beyond one year are classified as Marketable securities, non-current, on the Consolidated Balance Sheets.

As of December 31, 2025 and 2024 the Company’s marketable securities were classified as available-for-sale securities, carried at fair value, with the unrealized holding gains/(losses), net of income taxes, reflected in accumulated other comprehensive income/(loss) until realized. Regardless of the intent to sell a security, the Company performs additional analysis on all securities with unrealized losses to evaluate losses associated with the creditworthiness of the security. Credit losses are recorded when the Company does not expect to receive cash flows sufficient to recover the amortized cost basis of a security. For the purposes of computing realized and unrealized gains and losses, cost and fair value are determined on a specific identification basis. Purchase premiums and discounts on marketable debt securities are amortized or accreted into the cost basis over the life of the related security as adjustments to the yield using the effective-interest method.

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Dividends on marketable securities are recognized as income when declared and are recorded as Dividend income in the Consolidated Statements of Operations and Comprehensive Loss. Interest income is recognized when earned.

For further discussion related to marketable securities, please refer to Note 3. Investments in Marketable Securities.

Inventory

Inventory valuation is established based on a number of factors including, but not limited to, finished goods not meeting product specifications, product excess and obsolescence, or application of the lower of cost or net realizable value concepts. The determination of events requiring the establishment of inventory valuation, together with the calculation of the amount of such adjustments may require judgment. The Company performs an assessment of the recoverability of capitalized inventory during each reporting period and, if needed, records a write-down of inventory to its estimated net realizable value in the period it is identified. For further discussion related to inventory, please refer to Note 5. Inventory.

Prepaid Expenses and Other Current Assets

Prepaid expenses and other current assets include amounts paid in advance for operating expenses as well as monies to be received from the country of France and the State of Connecticut for research and development tax credits. These research and development tax credits are exchanged for a cash refund and are typically collected within one year from the date the tax return is filed with the state. The credits are recognized as an offset to research and development expenses in the Consolidated Statements of Operations and Comprehensive Loss in the annual period the corresponding expenses were incurred.

Property and Equipment, Net

Property and equipment are stated at cost less accumulated depreciation and amortization. Depreciation expense is computed using the straight-line method over the estimated useful lives of the related assets. Leasehold improvements are amortized over the shorter of the asset’s useful life or the life of the lease term.

Estimated useful lives of property and equipment are as follows:

Property and equipment, net Estimated useful life

Laboratory and production equipment 3-5 years

Computer equipment 3-5 years

Software 3 years

Furniture and fixtures 3-7 years

Expenditures for major renewals and improvements are capitalized. Expenditures for repairs and maintenance are expensed as incurred. Costs for property and equipment not yet placed into service have been recorded as construction in process and will be depreciated in accordance with the above guidelines once placed into service. When assets are retired or otherwise disposed of, the cost of these assets and related accumulated depreciation and amortization is eliminated from the balance sheet, and any resulting gains or losses are included in the Consolidated Statements of Operations and Comprehensive Loss in the period of disposal.

Capitalized Software Development Costs

The Company capitalizes certain internal use software development costs related to its SaaS platform incurred during the application development stage when management with the relevant authority authorizes and commits to the funding of the project, it is probable the project will be completed, and the software will be used as intended. The Company also capitalizes costs related to specific upgrades and enhancements when it is probable the expenditure will result in additional functionality. Costs related to preliminary project activities and to post-implementation activities are expensed as incurred.

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Internal use software is amortized on a straight-line basis over its estimated useful life, which is generally two years. Management evaluates the useful lives of these assets on an annual basis and tests for impairment whenever events or changes in circumstances occur that could impact the recoverability of the assets. Capitalized costs are recorded as Internally developed software on the Consolidated Balance Sheets. Amortization expense related to internally developed software was $0.6 million and $0.2 million for the years ended December 31, 2024 and 2023, respectively. As of December 31, 2024, the Company’s capitalized software was fully amortized and there was no such amortization expense for the year ended December 31, 2025.

Impairment of Long-Lived Assets

The Company reviews its long-lived assets for impairment when the Company determines a triggering event has occurred. When a triggering event has occurred, each impairment test is based on a comparison of the future expected undiscounted cash flows to the recorded value of the asset. If the recorded value of the asset is less than the undiscounted cash flows, the asset is written down to its estimated fair value.No impairments were recorded for the years ended December 31, 2025, 2024 and 2023.

Leases

The company currently leases executive office space in Branford, Connecticut, office, laboratory and manufacturing space in San Diego, California and semiconductor chip assembly and packaging space in Garnet Valley, Pennsylvania. The Company’s current leases expire at various dates through 2029.

The Company’s real estate lease agreements may include options to either renew and/or early terminate the lease. Leases with renewal options allow the Company to extend the lease term typically between 1 and 5 years. When it is reasonably certain that the Company will exercise an option to renew or terminate a lease, these options are considered in determining the classification and measurement of the lease at lease commencement.

The Company’s leases generally do not have a readily determinable implicit discount rate. As such, the Company uses an incremental borrowing rate based on the information available at the lease commencement date to determine the present value of the lease payments. The Company’s incremental borrowing rate is the estimated rate that would be required to pay for a collateralized borrowing equal to the total lease payment over the lease term. The Company measures right-of-use (“ROU”) assets based on the corresponding lease liability adjusted for (i) payments made to the lessor at or before the commencement date, (ii) initial direct costs incurred and (iii) tenant incentives under the lease. The Company’s lease terms may include options to extend or terminate the lease when it is reasonably certain it will exercise that option. Lease expense for minimum lease payments is recognized on a straight-line basis over the lease term for operating leases. Finance leases will result in a front-loaded expense pattern. With respect to finance leases, amortization of the ROU asset is presented separately from interest expense related to the finance lease liability. In addition, the Company does not have significant residual value guarantees or restrictive covenants in the lease portfolio.

Certain of the Company’s lease agreements contain tenant improvement incentives and allowances, rent holidays, or rent escalation clauses. For tenant improvement incentives, if the incentive is determined to be a leasehold improvement owned by the lessee and the Company is reasonably certain to use the incentive, the Company generally records the incentive as a reduction to the fixed lease payments liability as a reduction to lease cost. Reimbursable construction costs incurred are recorded as leasehold improvements and are amortized over the term of the lease. The Company records rental expense related to rent holidays and rent escalation clauses on a straight-line basis over the term of the lease. The Company uses the date of initial possession as the commencement date for lease incentives, which is generally when the Company is given right of access to the space and begins to make improvements in preparation for intended use.

Upon inception, leases are evaluated and classified as operating or finance for financial reporting purposes. Operating leases that are short term in nature and have month-to-month payment terms are expensed as incurred in Research and development expenses or in Selling, general and administrative expenses in the Consolidated Statements of Operations and Comprehensive Loss. The Company’s lease agreements contain variable lease costs for common area maintenance, utilities, taxes and insurance, which are expensed as incurred.

Warrant Liabilities

The Company’s outstanding warrants include publicly traded warrants (the “Public Warrants”) which were issued as one-third of one redeemable warrant per unit issued during HighCape’s initial public offering on September 9, 2020, and

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warrants sold in a private placement (the “Private Warrants”) to HighCape’s sponsor, HighCape Capital Acquisition LLC (the “Sponsor”). The Public Warrants and Private Warrants meet the definition of a derivative and the Company recorded these warrants as long-term liabilities on the Consolidated Balance Sheets at fair value upon the closing of the Business Combination, with subsequent changes in their respective fair values recognized in the Consolidated Statements of Operations and Comprehensive Loss at each reporting date. As of December 31, 2025, the warrants are classified as current liabilities on the Consolidated Balance Sheets. For further discussion related to the Public Warrants and Private Warrants, please refer to Note 11. Warrant Liabilities.

Warranty

The Company provides a free one-year assurance-type warranty to customers with the initial purchase of a Platinum instrument. The cost of the warranty is accrued upon the initial sale of an instrument in Accrued expenses and other current liabilities on the Consolidated Balance Sheets.

Revenue Recognition

The Company’s revenue is derived from sales of products and services. Product revenue is primarily generated from the sales of instruments and consumables used in protein sequencing and analysis. Service revenue is primarily generated from service maintenance contracts including access to analysis software and advanced training for instrument use. The Company recognizes revenue when or as a customer obtains control of the promised goods and services. The amount of revenue recognized reflects the consideration to which the Company expects to be entitled in exchange for these goods and services. This process involves identifying the contract with a customer, determining the performance obligations in the contract, determining the contract price, allocating the contract price to the distinct performance obligations in the contract, and recognizing revenue as the performance obligations have been satisfied. The Company has made the accounting policy election allowed for under ASC 606-10-32-2A to exclude all sales taxes from transaction price. Revenue recognition for contracts with multiple deliverables is based on the separate satisfaction of each distinct performance obligation within the contract. A performance obligation is considered distinct from other obligations in a contract when it provides a benefit to the customer either on its own or together with other resources readily available to the customer and is separately identified in the contract. The Company allocates transaction price to the performance obligations in a contract with a customer based on the relative standalone selling price of each performance obligation. The Company determines standalone selling price based on the price at which the performance obligation is sold separately. If the standalone selling price is not observable through past transactions, the Company estimates the standalone selling price taking into account available information and specific factors such as competitive positioning, internal costs, profit objectives, and internally approved pricing guidelines related to the performance obligation.

The Company considers performance obligation for sales of products satisfied upon shipment of the goods to the customer in accordance with the shipping terms (either upon shipment or delivery), which is when control of the product is deemed to be transferred; this includes instruments and consumables. Customers generally do not have a right to return products, except for defective or damaged products during the warranty period or unless prior written consent is provided. In instances where right of payment or transfer of title is contingent upon the customer’s acceptance of the product, revenue is deferred until all acceptance criteria have been met. Revenues for service maintenance contracts, which start after the first year of purchase and are considered as service type warranties that effectively extend the standard first-year service coverage at the customer’s option are recognized ratably over the contract service period as these services are performed evenly over time. Revenues for advanced training is recognized at a point in time upon satisfaction of the underlying performance obligation. The Company typically provides a standard one-year warranty which covers defects in materials, workmanship and manufacturing or performance conditions under normal use and service. The first year of the warranty of the products is considered an assurance-type warranty and is recorded as Cost of revenue within the Consolidated Statements of Operations and Comprehensive Loss. The Company has determined the standard first-year warranty is not a distinct performance obligation.

The Company disaggregates revenue from contracts with customers by type of revenue. The Company believes product revenue and service revenue aggregate the payor types by nature, amount, timing and uncertainty of its revenue streams. For further discussion on the disaggregation of revenue, please refer to Note 15. Segment Information.

Deferred Revenue

Deferred revenue primarily consists of billings and payments received in advance of revenue recognition from service maintenance contracts including software subscription and advanced training, and is reduced as the revenue recognition

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criteria are met. Deferred revenue also includes advanced training provided to customers until the service has been performed. Deferred revenue that will be recognized as revenue within the succeeding 12-month period is recorded as current and is included within Accrued expenses and other current liabilities in the Company’s Consolidated Balance Sheets. The portion of deferred revenue where revenue is expected to be recognized beyond twelve months from the reporting date is recorded as non-current deferred revenue and is included in Other long-term liabilities in the Company’s Consolidated Balance Sheets.

As of December 31, 2025, the Company had deferred revenue of $0.1 million included within Accrued expenses and other current liabilities in the Company’s Consolidated Balance Sheets. As of December 31, 2025, amounts included within Other long-term liabilities in the Company’s Consolidated Balance Sheets were immaterial. The Company expects to recognize approximately 80% of its remaining performance obligations as revenue during the year ending December 31, 2026.

Shipping and Handling Costs

Shipping and handling costs associated with outbound freight after control of a product has transferred to a customer are accounted for as fulfillment costs and are included in Cost of revenue in the Consolidated Statements of Operations and Comprehensive Loss. Shipping and handling costs billed to customers are considered part of the transaction price and are recognized as revenue with the underlying product sales.

Research and Development

Research and development expenses primarily consist of personnel costs and benefits, stock-based compensation, lab supplies, consulting and professional services, fabrication services, facilities costs, software, and other outsourced expenses. Research and development expenses are expensed as incurred and are primarily related to the development of new products and services.

Selling, General and Administrative

Net Loss per Share

Basic net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted-average number of shares of Class A and Class B common stock of the Company outstanding during the period, without consideration of potentially dilutive securities.

Diluted net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted average number of Class A and Class B common shares plus the common equivalent shares of the period, including any dilutive effect from such shares. The Company’s diluted net loss per share is the same as basic net loss per share for all periods presented, since the effect of potentially dilutive securities is anti-dilutive.For further discussion, please refer to Note 12. Net Loss Per Share.

Stock-Based Compensation

Stock-based compensation expense for restricted stock and stock option grants with only service conditions is recognized on a straight-line basis over the requisite service period of the individual grants, which is generally the vesting period, based on the estimated grant date fair values. Stock-based compensation expense for stock option grants subject to non-

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financing event performance conditions on an accelerated basis is recognized as though each vesting portion of the award was, in substance, a separate award.

The fair value of restricted stock is estimated using the current market price of the Company’s common stock on the date of grant.

The Company measures compensation expense for stock-based awards to employees, non-employees and directors based upon the awards’ initial grant-date fair values. Stock-based compensation expense for stock options, restricted stock units and performance awards is recorded over the requisite service period. For awards with only a service condition, the Company expenses stock-based compensation using the straight-line method over the requisite service period for the entire award. For awards with a market condition, the Company expenses the grant date fair value at the target over the vesting period regardless of the value the award recipients ultimately receive. The fair value of restricted stock without a market condition is estimated using the current market price of the Company’s common stock on the date of grant. The fair value of stock option grants with a market condition is estimated at the date of grant using the Monte Carlo simulation model (“Monte Carlo”). The fair values of stock option grants with only a service condition are estimated as of the date of grant by applying the Black-Scholes option valuation model (“Black-Scholes model”). The Black-Scholes model and Monte Carlo models incorporate assumptions as to stock price volatility, the expected life of options or restricted stock, a risk-free interest rate and dividend yield. The effect of forfeiture in compensation costs is recognized based on actual forfeitures when they occur.

•Expected Term: The expected term is calculated using the weighted-average period that the stock options are expected to be outstanding prior to being exercised. The Company determines expected term based on historical exercise patterns and its expectation of the time it will take for employees to exercise options still outstanding. The Company estimates non-employees’ options based on the contractual term.

•Risk-free Interest Rate: The risk-free interest rate for periods within the expected term of the awards is based on the U.S. Treasury yield curve in effect at the time of the grant.

•Expected Stock Price Volatility: The Company determined expected annual equity volatility based on the combination of the historical volatility of its common stock and the historical volatility of the common stock comparable to the Company’s common stock.

•Dividend Yield: Because the Company has never paid a dividend and does not expect to begin doing so in the foreseeable future, the Company assumes no dividend yield in valuing the stock-based awards.

•Exercise Price: The exercise price is taken directly from the grant notice issued to employees and non-employees.

Income Taxes

The Company utilizes the asset and liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are recognized for the expected future tax consequences of temporary differences between the carrying amounts and the tax basis of assets and liabilities using the enacted statutory tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. A valuation allowance is established against net deferred tax assets if, based on the weight of available evidence, it is more likely than not some or all of the net deferred tax assets will not be realized.

The Company accounts for uncertainty in income taxes recognized in the financial statements by applying a two-step process to determine the amount of tax benefit to be recognized. First, the tax position must be evaluated to determine the likelihood it will be sustained upon external examination by the taxing authorities. If the tax position is deemed more-likely-than-not-to be sustained, the tax position is then assessed to determine the amount of benefit to recognize in the financial statements. The amount of the benefit that may be recognized is the largest amount that has a greater than 50% likelihood of being realized upon ultimate settlement. The provision for income taxes includes the effects of any resulting tax reserves or unrecognized tax benefits that are considered appropriate, as well as the related net interest and penalties, as applicable. As of both December 31, 2025 and 2024,no accrued interest and penalties associated with any uncertain tax

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positions were recorded on the Consolidated Balance Sheets. The Company recognized an immaterial amount of interest and penalties in the Statements of Operations and Comprehensive Income for the year ended December 31, 2024. There were no interest and penalties recognized in the Statements of Operations and Comprehensive Income for the years ended December 31, 2025 and December 31, 2023.

Recently Issued Accounting Pronouncements

In July 2025, the FASB issued ASU 2025-05, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses for Accounts Receivable and Contract Assets. This standard provides entities with a practical expedient when calculating current expected credit loss by assuming the current conditions as of the balance sheet date will not change for the remaining life of the asset. The ASU is effective for fiscal years beginning after December 15, 2025 and interim periods within those annual periods, with early adoption permitted. The ASU is to be applied on a prospective basis. The Company adopted ASU 2025-05 effective January 1, 2026. The adoption of ASU 2025-05 did not have a material impact to the Consolidated Financial Statements and disclosures.

In November 2024, the FASB issued ASU No. 2024-03, Disaggregation of Income Statement Expenses (“DISE”), which requires additional disclosure of the nature of expenses included in the income statement. The ASU requires disclosures about specific types of expenses included in the expense captions presented on the face of the income statement as well as disclosures about selling expenses. The amendments in this update are effective for annual reporting periods beginning after December 15, 2026 and interim reporting periods beginning after December 15, 2027, with early adoption permitted. The ASU is required to be applied prospectively with the option for retrospective application. The Company is currently evaluating the impact ASU 2024-03 may have on its Consolidated Financial Statements and disclosures.

In March 2024, the FASB issued ASU No. 2024-02, Codification Improvements - Amendments to Remove References to the Concepts Statements, which contains amendments to the Codification that remove references to various Concepts Statements. The amendments in ASU 2024-02 are not intended to result in significant accounting changes for most entities. The Company adopted ASU 2024-02 effective January 1, 2025. The adoption of ASU 2024-02 did not have a material impact to the Consolidated Financial Statements and disclosures.

In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures, which expands income tax disclosure requirements to include additional information related to the rate reconciliation of effective tax rates to statutory rates, as well as additional disaggregation of taxes paid in both U.S. and foreign jurisdictions. The amendments in ASU 2023-09 also remove disclosures related to certain unrecognized tax benefits and deferred taxes. The Company adopted ASU 2023-09 prospectively during the year ended December 31, 2025. The impact of ASU 2023-09 was not material to the Company’s Consolidated Financial Statements. For further details regarding the Company’s income taxes, please refer to Note 14. Income Taxes.

Note 3. Investments in Marketable Securities

During the year ended December 31, 2023, the Company’s investments in marketable securities were classified as trading securities and consisted of ownership interests in fixed income mutual funds. In the fourth quarter of 2023, these trading securities were sold and the Company reinvested the funds received from the sale in marketable securities deemed to be available-for-sale securities. Unrealized gain (loss) on trading securities and realized loss on trading securities related to the Company’s trading securities for the years ended December 31, 2025, 2024 and 2023 were as follows (in thousands):

Unrealized gain on trading securities $ — $ — $ 10,690

Realized loss on trading securities $ — $ — $ (5,103)

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The following is a summary of the Company’s available-for-sale securities recorded within Marketable securities on the Consolidated Balance Sheets as of December 31, 2025 and 2024 (in thousands):

AmortizedCosts GrossUnrealized Net Gains/(Losses) FairValue

Financial Assets

Short-term marketable securities:

Long-term marketable securities:

AmortizedCosts GrossUnrealizedNet Gains FairValue

Financial Assets

Short-term marketable securities:

The fair values of the Company’s available-for-sale securities included within Marketable securities on the Consolidated Balance Sheets as of December 31, 2025 and 2024, by remaining contractual maturity, are as follows (in thousands):

One Yearor Less OverOne YearThroughFive Years Total

Financial Assets

Short-term marketable securities:

Long-term marketable securities

Total long-term marketable securities — 52,855 52,855

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One Yearor Less Total

Financial Assets

Short-term marketable securities:

Note 4. Fair Value of Financial Instruments

Fair value estimates of financial instruments are made at a specific point in time, based on relevant information about financial markets and specific financial instruments. As these estimates are subjective in nature, involving uncertainties and matters of significant judgment, they cannot be determined with precision. Changes in assumptions can significantly affect estimated fair value.

The Company measures fair value as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in an orderly transaction between market participants at the reporting date. The Company utilizes a three-tier hierarchy, which prioritizes the inputs used in the valuation methodologies in measuring fair value:

•Level 1: Valuations based on quoted prices in active markets for identical assets or liabilities that an entity has the ability to access.

•Level 2: Valuations based on quoted prices for similar assets or liabilities, quoted prices for identical assets or liabilities in markets that are not active, or other inputs that are observable or can be corroborated by observable data for substantially the full term of the assets or liabilities.

•Level 3: Valuations based on inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

The carrying value of cash and cash equivalents, accounts payable and accrued expenses and other current liabilities approximates their fair values due to the short-term or on demand nature of these instruments. As of December 31, 2025 and 2024, the Company’s investment portfolio included available-for-sale securities which were comprised of money market funds, U.S. Treasury bills, U.S. government agency bonds and/or commercial paper. The Company has certain U.S. Treasury bills, U.S. government agency bonds, and commercial papers classified as Level 2 due to the fair value for these instruments being determined by utilizing observable inputs in similar assets or identical assets in non-active markets.

Warrants are recorded as Warrant liabilities, current, and Warrant liabilities, non-current, on the Consolidated Balance Sheets as of December 31, 2025 and December 31, 2024, respectively. The warrant liabilities are measured at fair value at inception and on a recurring basis, with changes in fair value presented as Change in fair value of warrant liabilities in the Consolidated Statements of Operations and Comprehensive Loss.

The Public Warrants and Private Warrants were carried at fair value as of December 31, 2025 and 2024. The Public Warrants were valued using Level 1 inputs as they are traded in an active market. The Private Warrants were valued using a binomial lattice model, which results in a Level 3 fair value measurement. The primary unobservable input utilized in determining the fair value of the Private Warrants was the expected volatility of the Company’s Class A common stock. The expected volatility was based on consideration of the implied volatility from the Company’s own public warrant pricing and on the historical volatility observed at guideline public companies. As of December 31, 2025, the significant assumptions used in preparing the binomial lattice model for valuing the Private Warrants liability include (i) volatility of 263.6%, (ii) risk-free interest rate of 3.60%, (iii) strike price of $11.50, (iv) fair value of common stock of $1.10, and (v) expected life of 0.4 years. As of December 31, 2024, the significant assumptions used in preparing the binomial lattice model for valuing the Private Warrants liability include (i) volatility of 194.3%, (ii) risk-free interest rate of 4.20%, (iii) strike price of $11.50, (iv) fair value of common stock of $2.70, and (v) expected life of 1.4 years.

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The following tables set forth the Company’s fair value hierarchy for assets and liabilities measured at fair value as of December 31, 2025 and 2024 (in thousands):

Level 1 Level 2 Level 3 Total

Financial Assets:

Cash equivalents:

Marketable securities:

Liabilities:

Public Warrants $ 767 $ — $ — $ 767

Private Warrants — — 27 27

Total liabilities at fair value on a recurring basis $ 767 $ — $ 27 $ 794

Level 1 Level 2 Level 3 Total

Financial Assets:

Cash equivalents:

U.S. Treasury securities — — — —

Marketable securities:

Liabilities:

Total liabilities at fair value on a recurring basis $ 4,792 $ — $ 203 $ 4,995

There were no transfers of financial assets or liabilities into or out of Level 3 for the years ended December 31, 2025 and 2024.

Note 5. Inventory

Inventory consists of the following as of December 31, 2025 and 2024 (in thousands):

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Charges recorded for inventory write-downs included in Research and development expenses in the Consolidated Statements of Operations and Comprehensive Loss were $1.6 million, $3.2 million and $3.4 million for the years ended December 31, 2025, 2024 and 2023, respectively.

Charges recorded for inventory write-downs included in Cost of revenue in the Consolidated Statements of Operations and Comprehensive Loss were $0.7 million and $0.2 million for the years ended December 31, 2025 and 2024, respectively. Charges recorded for inventory write-downs included in Cost of revenue in the Consolidated Statements of Operations and Comprehensive Loss were immaterial for the year ended December 31, 2023.

Note 6. Property and Equipment, Net

Property and equipment, net, consists of the following as of December 31, 2025 and 2024 (in thousands):

Laboratory and production equipment $ 14,615 $ 13,412

Purchased software 57 57

Less: Accumulated depreciation and amortization (16,737) (11,707)

Depreciation and amortization expense is included within Cost of revenue, Research and development and Selling, general and administrative expenses in the Consolidated Statements of Operations and Comprehensive Loss. For the years ended December 31, 2025, 2024 and 2023, depreciation and amortization expense was $4.5 million, $4.6 million and $4.2 million, respectively.

For the year ended December 31, 2025, the Company recorded immaterial losses on disposals relating to property and equipment of $0.1 million with accumulated depreciation and amortization of $0.1 million. For the year ended December 31, 2024, the Company recorded losses on disposals of $0.4 million relating to property and equipment of $3.2 million with accumulated depreciation and amortization of $2.8 million. For the year ended December 31, 2023, the Company recorded losses on disposals of $0.1 million relating to property and equipment of $0.3 million with accumulated depreciation and amortization of $0.2 million.

Note 7. Leases

Lease-related costs for the years ended December 31, 2025,2024 and 2023 are as follows (in thousands):

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As of December 31, 2025, the maturities of the operating lease liabilities and a reconciliation to the present value of lease liabilities were as follows (dollars in thousands):

RemainingLease Payments

Total remaining undiscounted lease payments $ 4,554

Less: Imputed interest (388)

Total operating lease liabilities 4,166

Less: current portion (1,844)

Long-term operating lease liabilities $ 2,322

Weighted-average remaining lease term (in years) 2.2

Weighted-average discount rate 8.1 %

The following table provides certain cash flow and supplemental cash flow information related to the Company’s right-of-use assets and lease liabilities for the years ended December 31, 2025 and 2024 (in thousands):

Operating cash paid to settle operating lease liabilities $ 3,910 $ 4,436

Right-of-use assets obtained in exchange for lease liabilities(1) $ — $ 1,047

(1) The year ended December 31, 2024 includes an increase in right-of-use assets due to the change in estimated timing of receipt of reimbursements for tenant improvements related to the New Haven, Connecticut lease.

During the year ended December 31, 2025, the Company entered into the Mutual Release Agreement to terminate the lease of 67,000 square feet of space in New Haven, Connecticut, resulting in the derecognition of the right-of-use asset in the amount of $7.3 million and the related lease liability in the amount of $5.6 million which were included in Operating lease right-of-use assets and Operating lease liabilities, respectively, on the Consolidated Balance Sheets. For further details regarding this lease termination, please refer to Note 17. Commitments and Contingencies.

Note 8. Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consist of the following as of December 31, 2025 and 2024 (in thousands):

Restructuring costs — 679

Severance costs 137 —

Total accrued expenses and other current liabilities $ 1,505 $ 4,848

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Note 9. Equity Transactions

Class A Common Stock

As of December 31, 2025 and 2024, the Company had authorized 600,000,000 shares of Class A common stock at $0.0001 par value per share, of which a total of 196,431,273 and 146,953,271 shares were outstanding, respectively.

Voting Rights

Holders of Class A common stock will be entitled to cast one vote per Class A share. Generally, holders of all classes of common stock vote together as a single class, and an action is approved by stockholders if a majority of votes cast affirmatively or negatively on the action are cast in favor of the action, while directors are elected by a plurality of the votes cast. Holders of Class A common stock will not be entitled to cumulate their votes in the election of directors.

Class B Common Stock

As of December 31, 2025 and 2024, the Company had authorized 27,000,000 shares of Class B common stock at $0.0001 par value per share, of which a total of 19,937,500 shares were outstanding for both years.

Voting Rights

Holders of Class B common stock will be entitled to cast 20 votes per share of Class B common stock. Generally, holders of all classes of common stock vote together as a single class, and an action is approved by stockholders if a majority of votes cast affirmatively or negatively on the action are cast in favor of the action, while directors are elected by a plurality of the votes cast. Holders of Class B common stock will not be entitled to cumulate their votes in the election of directors.

Dividend Rights of Class A and Class B Common Stock

With limited exceptions in the case of certain stock dividends or disparate dividends approved by the affirmative vote of the holders of a majority of the Class A common stock and Class B common stock, each voting separately as a class, holders of Class B common stock will share ratably (based on the number of shares of Class B common stock held), together with each holder of Class A common stock, if and when any dividend is declared by the Board out of funds legally available therefor, subject to restrictions, whether statutory or contractual (including with respect to any outstanding indebtedness), on the declaration and payment of dividends and to any restrictions on the payment of dividends imposed by the terms of any outstanding preferred stock or any class or series of stock having a preference over, or the right to participate with, the Class B common stock with respect to the payment of dividends.

Preferred Stock

As of December 31, 2025 and 2024, the Company had authorized 1,000,000 shares of preferred stock at $0.0001 par value per share. There were no preferred shares outstanding for both years.

Preferred stock may be issued from time to time in one or more series. Any shares of preferred stock which may be redeemed, purchased or acquired by the Company may be reissued except as otherwise provided by law.

At-the-Market Equity Offering Programs

The Company filed a universal shelf registration statement on Form S-3 and a subsequent amendment to the Form S-3 (the “2025 Shelf Registration Statement”), on September 26, 2025 and October 9, 2025, respectively, covering the offering of Class A common stock, preferred stock, debt securities, warrants, rights and units. The 2025 Shelf Registration Statement replaced an equivalent shelf registration statement on Form S-3 originally declared effective on August 22, 2023 (the “2023 Shelf Registration Statement”).

On September 26, 2025, the Company entered into a Sales Agreement (the “Leerink Sales Agreement”) with Leerink Partners LLC (“Leerink”), pursuant to which the Company may offer and sell shares of its Class A common stock, having an aggregate offering price of up to $100.0 million, from time to time through an “at-the-market” offering program under which Leerink will act as sales agent (the “2025 ATM Offering”). The Company has no obligation to sell any shares under the Leerink Sales Agreement and may at any time suspend solicitation and offers under the Leerink Sales Agreement. The

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2025 ATM Offering is being made pursuant to the 2025 Shelf Registration Statement and a sales agreement prospectus related to the 2025 ATM Offering. During the year ended December 31, 2025, there were no shares sold under the Sales Agreement.

On December 11, 2024, the Company entered into an Equity Distribution Agreement (the “Canaccord Sales Agreement”) with Canaccord Genuity LLC (“Canaccord”) to sell shares of its Class A common stock having an aggregate offering price of up to $75.0 million, from time to time through an “at-the-market” offering program under which Canaccord acted as sales agent (the “2024 ATM Offering”). The Company had no obligation to sell any shares under the Canaccord Sales Agreement and could at any time suspend solicitation and offers under the Canaccord Sales Agreement. The 2024 ATM Offering was made pursuant to the 2023 Shelf Registration Statement and a prospectus supplement related to the 2024 ATM Offering dated December 11, 2024. During the year ended December 31, 2024, we sold and issued 23,425,650 shares of our Class A common stock under the 2024 ATM Offering, resulting in gross proceeds of $36.2 million. Net proceeds were $34.8 million after commissions and issuance costs of $1.4 million. The Company sold no shares of our Class A common stock under the 2024 ATM Offering during the years ended December 31, 2025 and December 31, 2023. In connection with the July 2025 Registered Direct Offering, as described below, the Company provided written notice, effective as of July 3, 2025, to Canaccord of its election to terminate the Canaccord Sales Agreement for its at-the-market offering.

Registered Direct Offerings and Pre-funded Warrants

On July 3, 2025, the Company entered into a securities purchase agreement with a certain institutional investor pursuant to which the Company agreed to issue and sell, in a registered direct offering (the “July 2025 Registered Direct Offering”), an aggregate of (i) 18,200,000 shares of the Company’s Class A common stock at a price of $1.67 per share and (ii) pre-funded warrants to purchase 11,740,119 shares of common stock (the “Pre-Funded Warrants”). The Pre-Funded Warrants were exercised in full on August 1, 2025 at the exercise price of $0.0001 for one share of Class A common stock per Pre-Funded Warrant. The gross proceeds to the Company from the July 2025 Registered Direct Offering were approximately $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by the Company, net proceeds as of December 31, 2025 were approximately $46.7 million.

On January 3, 2025, the Company entered into a securities purchase agreement with certain institutional investors pursuant to which the Company agreed to issue and sell, in a registered direct offering (the “January 2025 Registered Direct Offering”) an aggregate of 15,625,000 shares of the Company’s Class A common stock at a price of $3.20 per share. The gross proceeds to the Company from the January 2025 Registered Direct Offering were $50.0 million. After deducting estimated placement agents’ fees and other offering expenses payable by the Company, net proceeds recorded as of December 31, 2025 were approximately $46.8 million.

In connection with the Registered Direct Offerings, the Company entered into placement agency agreements with A.G.P./Alliance Global Partners (“AGP”), pursuant to which AGP agreed to serve as the sole placement agent for the Company on a reasonable best efforts basis. In connection with the Registered Direct Offerings, the Company agreed to pay AGP an aggregate cash fee equal to 6.0% of the gross proceeds received in the respective offering. The securities in both Registered Direct Offerings were sold pursuant to the Company’s universal shelf registration statement on Form S-3, which was originally filed with the SEC on August 11, 2023, and related base prospectuses and prospectus supplements dated July 3, 2025 and January 3, 2025, respectively, thereunder.

Note 10. Stock-based Compensation

Equity Incentive Plan

The Quantum-Si Incorporated 2021 Equity Incentive Plan (the “2021 Plan”) provides for grants of stock options, stock appreciation rights, restricted stock, restricted stock units, and other stock or cash-based awards. Directors, officers and other employees of the Company and its subsidiaries, as well as others performing consulting or advisory services for the Company, are eligible for grants under the 2021 Plan. As of December 31, 2025, there were 14,602,612 shares available for future grant under the 2021 Plan.

Inducement Equity Incentive Plan

On May 8, 2023, the Company adopted the 2023 Inducement Equity Incentive Plan (the “2023 Inducement Plan”) to reserve 3,000,000 shares of its Class A common stock to be used exclusively for grants of awards to individuals that were

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not previously employees or directors of the Company as a material inducement to such individuals’ entry into employment with the Company within the meaning of Rule 5635(c)(4) of the Nasdaq Listing Rules. On August 23, 2024, the Company amended the 2023 Inducement Plan to reserve an additional 3,000,000 shares of its Class A common stock under the 2023 Inducement Plan. The terms and conditions of the 2023 Inducement Plan, as amended, are substantially similar to those of the 2021 Plan. As of December 31, 2025, there were 2,239,404 shares remaining available for issuance under the 2023 Inducement Plan.

Stock options

The Company granted an aggregate of 1,166,855and 2,282,600 stock option awards to participants during the years ended December 31, 2025 and 2024, respectively, with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates.

During the year ended December 31, 2023, the Company granted an aggregate of 10,138,730 stock option awards to participants, with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates and, in specific instances, certain market conditions. These stock option awards included 2,000,000 stock options granted to the Chief Financial Officer which are subject to service and/or certain market conditions. The stock option awards granted to the Chief Financial Officer included 1,000,000 stock options issued from the 2021 Plan and 1,000,000 inducement stock options issued from the 2023 Inducement Plan which are subject to a service condition and certain market conditions. The service condition requires the Chief Financial Officer’s continued employment with the Company through the applicable vesting dates. The market conditions require the Company’s Class A common stock trade above a specified level for a defined period of time. The fair value of awards with market conditions was estimated at the grant date using the Monte Carlo simulation model.

Stock-based compensation related to stock options for the years ended December 31, 2025, 2024 and 2023 was $6.3 million, $6.4 million and $7.1 million, respectively. The Company estimates and records the compensation cost associated with the grants described above with an offsetting entry to paid-in capital. The Company utilized the Black-Scholes model for determining the estimated fair value for service or performance-based stock-based awards. The Black-Scholes model requires the use of subjective assumptions which determine the fair value of stock-based awards. The assumptions used to value option grants to employees and non-employees for the years ended December 31, 2025, 2024 and 2023 were as follows:

Expected dividend yield — — —

Weighted average fair value per share at grant date $1.17 $1.03 $1.01

A summary of the stock option activity is presented in the table below:

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The total fair value of stock options that vested during the years ended December 31, 2025 and 2024 was approximately $5.4 million and $6.4 million, respectively.

As of December 31, 2025 total unrecognized stock-based compensation related to stock options was $6.0 million, which is expected to be recognized over a remaining weighted average vesting period of 1.5 years.

Modification of Performance Stock Options

In November 2022 and May 2023, the Company granted 2,780,000 and 1,000,000 performance-based stock option awards to its Chief Executive Officer and Chief Financial Officer, respectively. The vesting of these awards are subject to continued service to the Company and certain market conditions. The market conditions require the Company’s Class A common stock trade above specified levels for certain periods of time. The fair values of the awards were estimated at the grant date using the Monte Carlo simulation model.

On March 15, 2024, the market conditions that trigger the vesting of these performance-based stock option awards were modified. The modified market conditions require the Company’s Class A common stock to trade above specified levels for certain defined periods of time that are different from the original awards. The Company accounted for the modifications as modifications of market conditions. The total incremental stock-based compensation expense to be recognized for these awards is approximately $2.4 million within Selling, general and administrative operating expenses in the Consolidated Statements of Operations and Comprehensive Loss. Incremental stock-based compensation expense was $0.8 million and $0.6 million for the years ended December 31, 2025 and 2024, respectively. There were no such modifications to performance-based stock option awards for the year ended December 31, 2023.

Restricted stock units

During the years ended December 31, 2025, 2024 and 2023, the Company granted an aggregate of 8,535,732, 9,216,559 and 786,938, respectively, of restricted stock unit (“RSU”) awards to participants with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates.

Stock-based compensation related to RSU awards for the years ended December 31, 2025, 2024 and 2023 was $4.5 million, $2.4 million and $1.4 million, respectively.

The number of shares and weighted average grant date fair values of restricted non-vested common stock at the beginning and end of 2025, as well as restricted stock units granted, vested, and forfeited during the year were as follows:

Number of SharesUnderlying RSUs Weighted AverageGrant-Date FairValue (per share)

As of December 31, 2025 total unrecognized stock-based compensation related to restricted stock was $13.4 million, which is expected to be recognized over the remaining weighted average vesting period of 2.9 years.

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The total fair value of restricted stock vested during the years ended December 31, 2025 and 2024 was approximately $4.2 million and $2.6 million, respectively.

Stock-based Compensation Expense

Stock-based compensation is allocated to Research and development and Selling, general and administrative operating expenses in the Consolidated Statements of Operations and Comprehensive Loss. Stock-based compensation expense for the years ended December 31, 2025, 2024 and 2023 is as follows (in thousands):

No related tax benefits of the stock-based compensation expense have been recognized and no related tax benefits have been realized from the exercise of stock options due to the Company’s net operating loss carryforwards.

Note 11. Warrant Liabilities

Public Warrants

As of December 31, 2025 and 2024, there was an aggregate of 3,833,317 and 3,833,319, respectively, of outstanding Public Warrants which entitle the holder to acquire Class A common stock. Each whole warrant entitles the registered holder to purchase one share of Class A common stock at an exercise price of $11.50 per share, subject to adjustment as discussed below, beginning on September 9, 2021. The warrants will expire on June 10, 2026 or earlier upon redemption or liquidation.

Redemptions

At any time while the warrants are exercisable, the Company may redeem not less than all of the outstanding Public Warrants:

•in whole and not in part;

•at a price of $0.01 per warrant;

•upon not less than 30 days’ prior written notice of redemption (the “30-day redemption period”) to each warrant holder; and

•if, and only if, the closing price of the Company’s common stock equals or exceeds $18.00 per share (as adjusted for stock splits, stock capitalizations, reorganizations, recapitalizations and the like) for any 20 trading days within a 30-trading day period ending three business days before the Company sends the notice of redemption to the warrant holders.

If the foregoing conditions are satisfied and the Company issues a notice of redemption of the Public Warrants at $0.01 per warrant, each holder of Public Warrants will be entitled to exercise his, her or its Public Warrants prior to the scheduled redemption date.

QSI US Equity

QSI · 10-K · period ended 2025-12-31

ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Item 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

QSI US Equity☆

QSI · 10-K · period ended 2025-12-31

ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Item 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

QSI US Equity