Quantum-Si Inc

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

Note 1. Description of Business and Basis of Presentation

Background

Quantum-Si Incorporated (including its subsidiaries, the “Company” or “Quantum-Si”) 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 through single-molecule sequencing. The Company has developed a proprietary, universal, single-molecule detection platform that is applied to proteomics to enable single-molecule protein sequencing 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 the ability to offer a fast analysis time has 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® single-molecule protein sequencing line of instruments, Platinum Analysis Software and consumable kits for use with the Platinum line of instruments.

The development of Proteus TM, the Company’s next-generation platform, was announced in November 2024 and is estimated to be launched in the second quarter of 2027. Proteus aims to provide single-molecule, amino acid level resolution while also providing anticipated significantly higher sequencing output per sample and increased sample throughput per run, automation of the sequencing workflow and automated data analysis as compared to Platinum Pro. The 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 an anticipated 80 million features. This new platform is expected to provide much deeper insights, while simplifying and significantly reducing the cost of the underlying consumable, with a wide range of proteomics applications that are addressable with our proprietary, single-molecule, kinetic detection technology.

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$765.5 million as of September 30, 2026. The Company has incurred significant operating losses, including net losses of$67.5 million and$83.7 million for thenine months ended September 30, 2026 and 2025, respectively. As of September 30, 2026, the Company had cash, cash equivalents and investments in marketable securities of $149.4 million. Management believes the Company’s cash, cash equivalents and marketable securities, together with revenue from the sales of its products and services, will be suffic ient to fund its planned operations for at least the next twelve months from the date of the issuance of the accompanying unaudited Condensed 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

The U.S. Federal Reserve has both lowered interest rates slightly in the third and fourth quarters of 2025, and then raised interest rates in the third quarter of 2026. It is not known whether additional action will be taken to lower or raise interest rates and if further changes will have an impact on overall 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 may 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.

Basis of Presentation and Principles of Consolidation

The accompanying unaudited Condensed 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.

These unaudited Condensed Consolidated Financial Statements should be read in conjunction with the audited Consolidated Financial Statements and the notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025. The Condensed Consolidated Balance Sheet as of December 31, 2025 included herein was derived from the audited Consolidated Financial Statements as of that date, but does not include all disclosures, including certain notes required by U.S. GAAP, on an annual reporting basis.

In the opinion of management, the accompanying unaudited Condensed Consolidated Financial Statements reflect all normal recurring adjustments necessary to fairly state the financial position, results of operations, and cash flows for the interim periods. The results for the three and nine months ended September 30, 2026 are not necessarily indicative of the results to be expected for any subsequent quarter, the year ending December 31, 2026, or any other period.

There have been no material changes to the Company’s significant accounting policies as described in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025.

Reclassifications

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

Note 2. Summary of Significant Accounting Policies

For the Company’s Significant Accounting Policies, please refer to its Annual Report on Form 10-K for the fiscal year ended December 31, 2025. Any reference in these notes to applicable guidance is meant to refer to the authoritative U.S. GAAP as found in the Accounting Standards Codification and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”).

Use of Estimates

The preparation of the unaudited Condensed Consolidated Financial Statements in conformity with U.S. GAAP requires the Company to make estimates and assumptions about future events that may affect the amounts recorded in its unaudited Condensed 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 unaudited Condensed Consolidated Financial Statements.

Restricted Cash

Restricted cash consists of deposits and other cash balances that are restricted as to withdrawal or use under the terms of certain contractual arrangements. As of September 30, 2026, restricted cash primarily consisted of$2.1 million in the form of a letter of credit held for the benefit of a landlord in connection with a lease, which is recorded within Restricted cash, non-current, on the Condensed Consolidated Balance Sheets. There was no such amount recorded as of December 31, 2025. For further information regarding restricted cash, please refer to Note 7. Leases.

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.

There are no additional ASUs issued and not yet adopted that are expected to have a material impact on the Company’s financial statements and related disclosures.

Note 3. Investments in Marketable Securities

As of September 30, 2026 and December 31, 2025, the Company’s investments in marketable securities were determined to be 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.

The following is a summary of the Company’s available-for-sale securities recorded within Marketable securities, current and non-current, on the Condensed Consolidated Balance Sheets as of September 30, 2026 and December 31, 2025 (in thousands):

The fair values of the Company’s available-for-sale securities included within Marketable securities, current and non-current, on the Condensed Consolidated Balance Sheets as of September 30, 2026 and December 31, 2025, by remaining contractual maturity, were as follows (in thousands):

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, restricted cash, 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 September 30, 2026 and December 31, 2025, 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, high-quality corporate bonds and commercial paper. The Company has U.S. Treasury bills, U.S. government agency bonds, corporate bonds and commercial paper that are 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 on the Condensed Consolidated Balance Sheets. The warrant liabilities were 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 Condensed Consolidated Statements of Operations and Comprehensive Loss.

The Company issued registered warrants (the “Public Warrants”) in connection with the initial public offering of HighCape as well as private placement warrants (the “Private Warrants”). The Public Warrants and Private Warrants were measured at fair value as of June 10, 2026 (the “Warrant Expiration Date”) and December 31, 2025. Prior to the Warrant Expiration Date, the Public Warrants were valued using Level 1 inputs as they were traded in an active market. The Private Warrants were valued using a binomial lattice model. 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 3.6%, (iii) strike price of $11.50, (iv) fair value of Class A common stock of $1.10, and (v) expected life of 0.4 years.

There were no exercises or redemptions of the Public Warrants or Private Warrants during thethree and nine months ended September 30, 2026 or 2025.

The following tables summarize the Company’s financial assets and liabilities on the Condensed Consolidated Balance Sheets as of September 30, 2026 and December 31, 2025, that are measured at fair value on a recurring basis, by level, within the fair value hierarchy (in thousands):

Note 5. Inventory

Inventory consists of the following as of September 30, 2026 and December 31, 2025 (in thousands):

There wereno charges for inventory write-downs recorded in Research and development expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss for the three months ended September 30, 2026. Such charges were $1.4 million for the nine months ended September 30, 2026. For the three and nine months ended September 30, 2025, such charges recorded were $0.4 million and $1.2 million, respectively.

There wereno charges for inventory write-downs recorded in Cost of revenue in the Condensed Consolidated Statements of Operations and Comprehensive Loss for the three months ended September 30, 2026. Such charges were immaterial for the nine months ended September 30, 2026. For the three and nine months ended September 30, 2025, such charges recorded were $0.3 million and $0.6 million, respectively.

Note 6. Property and Equipment, Net

Property and equipment, net, consists of the following as of September 30, 2026 and December 31, 2025 (in thousands):

Depreciation and amortization expense is included within Cost of revenue, Research and development and Selling, general and administrative expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Depreciation and amortization expense was $1.2 million for both the three months ended September 30, 2026 and 2025, and $3.6 million and $3.3 million for the nine months ended September 30, 2026 and 2025, respectively. No impairments of property and equipment were recorded for both the three and nine months ended September 30, 2026 or 2025.

Note 7. Leases

Lease-related costs for thethree and nine months ended September 30, 2026 and 2025 were as follows (in thousands):

Future minimum lease payments under non-cancellable leases as of September 30, 2026 were as follows (dollars in thousands):

The following table provides certain cash flow and supplemental cash flow information related to the Company’s lease liabilities for thenine months ended September 30, 2026 and 2025 (in thousands):

On June 18, 2026, the Company entered into a facility lease agreement (the “Lease Agreement”) with Sterling City Science South Development, LLC (the “Landlord”) for the lease of approximately 54,374 square feet of office, laboratory and manufacturing space located in San Diego, California.

Upon execution of the lease, the Company paid a security deposit of approximately $0.4 million, which is recorded in Other assets on the Condensed Consolidated Balance Sheets. The Company also provided an additional security deposit in the form of a letter of credit with an initial amount of approximately $2.1 million, which is recorded within Restricted cash, non-current, on the Condensed Consolidated Balance Sheets.

As of September 30, 2026, aggregate minimum cash lease payments under the Lease Agreement were approximately $38.3 million. These payments were not included in the future minimum lease payments table above as the lease had not commenced as of September 30, 2026.

The Lease Agreement also provided for a tenant improvement allowance of up to approximately $17.1 million. As of September 30, 2026, the Company had incurred approximately $0.7 million of costs eligible for reimbursement under the tenant improvement allowance.

Subsequently, on October 30, 2026, the Company entered into a Mutual Lease Termination and Settlement Agreement (the “Termination Agreement”) with the Landlord related to the aforementioned Lease Agreement. For further information regarding the Termination Agreement, please refer to Note 18. Subsequent Event.

Note 8. Accrued Expenses and Other Current Liabilities

As of September 30, 2026 and December 31, 2025, Accrued expenses and other current liabilities included on the Condensed Consolidated Balance Sheets consist of the following (in thousands):

Note 9. Equity Transactions

At-the-Market Equity Offering Program

The Company filed a universal shelf registration statement on Form S-3 and a subsequent amendment to the Form S-3 (the “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 September 26, 2025, the Company entered into a Sales Agreement (the “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 “ATM Offering”). The Company has no obligation to sell any shares under the Sales Agreement and may at any time suspend solicitation and offers under the Sales Agreement. The ATM Offering is being made pursuant to the Shelf Registration Statement and a sales agreement prospectus related to the ATM Offering. During the three and nine months ended September 30, 2026, there wereno shares sold under the Sales Agreement.

Preferred Stock

As of September 30, 2026 and December 31, 2025, the Company had authorized 1,000,000 shares of preferred stock at $0.0001 par value per share. There wereno preferred shares outstanding for both periods.

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.

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 September 30, 2026, there were 15,391,965 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 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 September 30, 2026, there were 1,787,825 shares available for future issuance under the 2023 Inducement Plan, as amended.

Stock Options

There wereno stock options awarded to participants during the three months ended September 30, 2026 and 2025. The Company granted participants an aggregate of 5,498,109 and 1,166,855 stock option awards to participants during the nine months ended September 30, 2026 and 2025, respectively, with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates.

The Company recorded $1.6 million for stock-based compensation related to stock options for both the three months ended September 30, 2026 and 2025, and $4.3 million and $4.8 million for stock-based compensation related to stock options for the nine months ended September 30, 2026 and 2025, respectively.

The fair value of each stock option award granted during the nine months ended September 30, 2026 was estimated as of the grant date using a Black-Scholes model with the following assumptions:

A summary of the stock option activity for the nine months ended September 30, 2026 is presented in the table below:

As of September 30, 2026, total unrecognized stock-based compensation related to stock options was $5.5 million, which is expected to be recognized over a remaining weighted average vesting period of 1.7 years.

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 is subject to continued service to the Company and certain market conditions. The market conditions require the Company’s Class A common stock to 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 within Selling, general and administrative operating expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss is approximately $2.4 million. Incremental stock-based compensation expense for these awards was $0.2 million for each of the three months ended September 30, 2026 and 2025 and $0.6 million for each of the nine months ended September 30, 2026 and 2025.

Restricted Stock Units

The Company granted participants an aggregate of 62,493 and 9,002,002 restricted stock unit (“RSU”) awards during the three and nine months ended September 30, 2026, respectively, to participants with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates. During the three and nine months ended September 30, 2025, the Company granted an aggregate of 254,101 and 8,435,844 RSU awards, respectively, to participants with vesting subject to the participant’s continued employment with or continued service provided to the Company through the applicable vesting dates.

The Company recorded $1.3 million and $1.2 million for stock-based compensation related to RSU awards for the three months ended September 30, 2026 and 2025, respectively, and $4.2 million and $3.3 million for stock-based compensation related to RSU awards for the nine months ended September 30, 2026 and 2025, respectively.

A summary of the RSU activity for the nine months ended September 30, 2026 is presented in the table below:

As of September 30, 2026, total unrecognized stock-based compensation related to restricted stock units was $12.6 million, which is expected to be recognized over the remaining weighted average vesting period of 2.8 years.

Stock-based Compensation Expense

Stock-based compensation is allocated to Research and development and Selling, general and administrative operating expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Stock-based compensation expense for the three and nine months ended September 30, 2026 and 2025 was allocated as follows (in thousands):

Note 11. Warrant Liabilities

Public Warrants

As of December 31, 2025, there was an aggregate of 3,833,317 outstanding Public Warrants. The Public Warrants did not meet the criteria to be classified in stockholders’ equity as the exercise of the Public Warrants could have been settled in cash upon the occurrence of a tender offer or exchange offer in which the maker of the tender offer or exchange offer, upon completion of the tender offer or exchange offer, beneficially owns more than 50% of the outstanding shares of the Company’s Class A common stock, even if it would not result in a change of control of the Company. This provision precluded the Public Warrants from being classified in equity and thus, they were classified as current liabilities on the Condensed Consolidated Balance Sheets as of December 31, 2025. These warrants expired on June 10, 2026 and, as of September 30, 2026, there wereno outstanding Public Warrants.

Private Warrants

As of December 31, 2025, there were 135,000 outstanding Private Warrants. The Private Warrants did not meet the criteria to be classified in stockholders’ equity as the terms of the Private Warrants provide for potential changes to the settlement amounts depending upon the characteristics of the warrant holder, and because the holder of a warrant is not an input into the pricing of a fixed-for-fixed option on equity shares. This provision precluded the Private Warrants from being classified in equity and thus, they were classified as current liabilities on the Condensed Consolidated Balance Sheets as of December 31, 2025. These warrants expired on June 10, 2026 and, as of September 30, 2026, there wereno outstanding Private Warrants.

As of December 31, 2025, the combined fair value of warrant liabilities was $0.8 million. There wereno such warrant liabilities as of September 30, 2026. The Company recognized a gain of $1.5 million for the three months ended September 30, 2025 as a Change in fair value of warrant liabilities in the Condensed Consolidated Statements of Operations and Comprehensive Loss. There was no such change for the three months ended September 30, 2026. The Company recognized gains of $0.8 million and $3.9 million for the nine months ended September 30, 2026 and 2025, respectively, as a Change in fair value of warrant liabilities in the Condensed Consolidated Statements of Operations and Comprehensive Loss.

There were no exercises or redemptions of the Public Warrants or Private Warrants during the three and nine months ended September 30, 2026 or 2025.

For further information regarding the warrant liabilities, please refer to Note 4. Fair Value of Financial Instruments.

Note 12. Net Loss Per Share

The Company presents both basic earnings per share (“EPS”) and diluted EPS. Basic and diluted net loss per share was the same for each period presented as the inclusion of all common share equivalents would have been anti-dilutive.

The following table presents the calculations for thethree and nine months ended September 30, 2026 and 2025 of basic and diluted net loss per share for the Company’s common stock (in thousands, except per share amounts):

Net loss per share attributable to Class A and Class B common stockholders was the same on a basic and diluted basis, as the inclusion of all potential common equivalent shares outstanding would have been anti-dilutive.

The following potential dilutive shares were excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive for thethree and nine months ended September 30, 2026 and 2025:

Note 13. Restructuring

In August 2026, the Company committed to an organizational restructuring to align resources and spending with the updated Proteus development program launch timing, while maintaining resources for critical development, manufacturing and commercial readiness activities. As of September 30, 2026, restructuring liabilities were approximately $1.2 million and are included in Accrued expenses and other current liabilities on the Condensed Consolidated Balance Sheets. There wereno restructuring liabilities recorded as of December 31, 2025.

The Company’s restructuring costs, primarily for cash severance and other severance costs, were allocated to the following operating expense categories as follows (in thousands):

(1) Restructuring charges incurred and cash payments and other adjustments include charges for cash severance and other severance costs, including health care coverage for a specified period of time after separation, and non-cash charges related to stock-based compensation expense.

The Company’s restructuring activities are expected to be completed by the end of the fourth quarter of 2026 and it does not expect to incur material additional charges associated with these activities.

Note 14. Income Taxes

Income taxes for thethree and nine months ended September 30, 2026 and 2025 were recorded at the Company’s estimated annual effective income tax rate, subject to adjustments for discrete events, if they occur. The Company’s estimated annual effective tax rate was 0.00% and 0.18%for thethree and nine months ended September 30, 2026, respectively. The Company’s estimated annual effective tax rate was(0.05)% and(0.06)%, for thethree and nine months ended September 30, 2025 respectively. The primary reconciling items between the federal statutory rate of 21.0% and the Company’s overall effective tax rate for these periods were related to the valuation allowance recorded against the Company’s U.S. net deferred tax assets.

A valuation allowance is required when it is more likely than not that some portion or all of the Company’s deferred tax assets will not be realized. The realization of deferred tax assets depends on the generation of sufficient future taxable income during the period in which the Company’s related temporary differences become deductible. Management believes that based on the earnings history of the Company, it is more likely than not that the benefits of these assets will not be realized, and therefore, a full valuation allowance has been recorded against the Company’s U.S. net deferred tax assets as of September 30, 2026 and December 31, 2025.

Note 15. Segment Information

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’s platform includes its Platinum single-molecule protein sequencing instrument, Platinum Analysis Software, and consumable kits for use with its Platinum line of instruments.

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 it operates as a single reportable segment. The CODM utilizes the Company’s long-range plan, which includes product development roadmaps and long-range financial models, as a key input to resource allocation. The CODM makes decisions on resource allocation, assesses the performance of the business, and monitors budget versus actual results on a consolidated basis using loss from operations as reported in the Condensed Consolidated Statements of Operations and Comprehensive Loss as the primary measure of segment profit or loss. Net loss and the change in cash and cash equivalents and marketable securities are also measures considered in monitoring budget versus actual results.

Significant expenses within loss from operations, as well as within net loss, include research and development, and selling, general and administrative expenses, which are each separately presented in the Company’s Condensed Consolidated Statements of Operations and Comprehensive Loss. Other segment items included in net loss on the Company’s Condensed Consolidated Statements of Operations and Comprehensive Loss are net lease termination expense, legal settlement expense, net of insurance proceeds, dividend income, interest income, change in fair value of warrant liabilities, other expense or income, net, and benefit or provision for income taxes.

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.

Total revenue generated from domestic and international sales for thethree and nine months ended September 30, 2026 and 2025 was as follows (in thousands):

Note 16. Related Party Transactions

The Company was a party to the Amended and Restated Technology Services Agreement (the “ARTSA”), most recently amended on November 11, 2020, by and among 4Catalyzer Corporation (“4C”), the Company and other participant companies controlled by Dr. Jonathan Rothberg, the former Chairman of the Board and current director. The Company entered into a First Addendum to the ARTSA on February 17, 2021 pursuant to which the Company agreed to terminate its participation under the ARTSA no later than immediately prior to the effective time of the Business Combination, resulting in the termination of the Company’s participation under the ARTSA on June 10, 2021. In connection with the termination of the Company’s participation under the ARTSA, the Company terminated its existing arm’s length lease agreement with 4C and negotiated an arm’s length lease agreement. Under the ARTSA, the Company and the other participant companies had agreed to share certain non-core technologies, which means any technologies, information or equipment owned or otherwise controlled by the participant company that are not specifically related to the core business area of the participant and subject to certain restrictions on use. The ARTSA also provided for 4C to perform certain services for the Company and each other participant company such as monthly administrative, management and technical consulting services to the Company which were pre-funded approximately once per quarter.

There wereno expenses paid to 4C for thethree and nine months ended September 30, 2026. There wereno expenses paid to 4C for the three months ended September 30, 2025. Expenses paid to 4C for the nine months ended September 30, 2025 were $0.1 million. These expenses included amounts for month-to-month sublease arrangements for office and laboratory spaces from 4C and certain administrative expenses and are included in Selling, general and administrative expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss.

The ARTSA also provided for the participant companies to provide other services to each other. As of both September 30, 2026 and December 31, 2025, there wereno amounts payable to or payable by the Company related to such services.

Note 17. Commitments and Contingencies

Commitments

Purchase Order Commitments

The Company has non-cancellable purchase order commitments for materials primarily related to research and development materials and inventory-related components under annual and multi-year agreements, some of which have minimum quantity requirements. These commitments are not recorded as liabilities in the Condensed Consolidated Balance Sheets as of September 30, 2026 as the Company had not yet received the related goods or services. As of September 30, 2026, the Company’s total purchase commitments under these agreements were $5.7 million, of which approximately $4.2 million and $1.5 million is estimated to be incurred during the years ended December 31, 2026 and 2027, respectively.

Licenses related to certain intellectual property

The Company licenses certain intellectual property, some of which may be utilized in its current or future product offerings. To preserve the right to use such intellectual property, the Company is required to make annual minimum fixed payments totaling approximately $0.1 million as well as royalties based on net sales if the royalties exceed annual minimum fixed payments. As of both September 30, 2026 and December 31, 2025, the Company had accrued royalties of approximately $0.1 million included in Accrued expenses and other current liabilities on the Condensed Consolidated Balance Sheets.

Other commitments

The Company sponsors a 401(k) defined contribution plan covering all eligible U.S. employees (the “401(k) Plan”). Contributions to the 401(k) Plan are discretionary. The Company didnot make any matching contributions to the 401(k) Plan for both thethree and nine months ended September 30, 2026 and 2025.

Contingencies

The Company is subject to claims in the ordinary course of business. Except as discussed below, the Company is not currently a party to any pending or threatened litigation, the outcome of which would be expected to have a material adverse effect on its financial condition, results of operations, or cash flows. The Company discloses contingent liabilities even if the liability is not probable or estimable, or both, if there is a reasonable possibility that a material loss may have been incurred.

Delaware Stockholder Litigation

On May 16, 2024, a putative class action lawsuit was filed in the Delaware Court of Chancery, styled Farzad v. HighCape Capital, et al. (the “Delaware Stockholder Litigation”). The Delaware Stockholder Litigation asserted breach of fiduciary duty claims against the former officers and directors of HighCape, including Kevin Rakin, Matt Zuga, David Colpman, Robert Taub and Antony Loebel, HighCape Capital Acquisition LLC and HighCape Capital L.P.; aiding and abetting breach of fiduciary duty claims against Foresite Capital Management, LLC and Dr. Rothberg; and unjust enrichment claims against all defendants related to the Business Combination. The Delaware Stockholder Litigation complaint alleged that the transactions contemplated by the Business Combination were a product of an unfair process which was allegedly impacted by conflicts of interest, resulting in mispricing of the Business Combination. Quantum-Si, as part of the Business Combination, had previously agreed to indemnify certain of the defendants related to actions such as the Delaware Stockholder Litigation to the extent allowable by law.

On July 22, 2025, the parties of the Delaware Stockholder Litigation, through a mediation process, reached a preliminary settlement. In connection with the preliminary settlement, the Company recorded an accrued legal settlement liability of $8.0 million, consisting of $7.6 million for the settlement and $0.4 million for legal and related expenses, as well as a legal settlement insurance receivable of $4.6 million on the Consolidated Balance Sheets as of December 31, 2025. The Company also recognized associated legal settlement expenses of $3.4 million recorded in legal settlement, net of insurance proceeds, in the Consolidated Statements of Operations and Comprehensive Loss for the year ended December 31, 2025.

Subsequently, on March 27, 2026, the Delaware Court of Chancery executed an order and final judgment approving the legal settlement. In the first quarter of 2026, the Company paid $3.0 million in connection with the settlement and the remaining $4.6 million was funded by insurance proceeds. Accordingly, the accrued legal settlement liability and associated legal settlement insurance receivable were derecognized from the Condensed Consolidated Balance Sheets in the first quarter of 2026.

Note 18. Subsequent Event

Lease Termination

On October 30, 2026, the Company entered into a Mutual Lease Termination and Settlement Agreement (the “Termination Agreement”) with Sterling City Science South Development, LLC (the “Landlord”). Under the Termination Agreement, the parties mutually terminated, effective that date, the lease agreement dated June 18, 2026 (the “Lease Agreement”) for approximately 54,374 rentable square feet of planned office, laboratory and manufacturing space at 9955 Pacific Heights

Boulevard, San Diego, California. The lease term had not yet commenced, and, accordingly, the Company had not recognized a right-of-use asset or lease liability associated with the Lease Agreement. As a result of the termination, the Company was released from approximately $38.3 million of aggregate minimum cash lease payments associated with the Lease Agreement. The Company hasno further obligations under the Lease Agreement.

Under the Termination Agreement, the Landlord is required to pay the Company approximately $1.3 million, consisting of $0.7 million for the reimbursement of costs incurred by the Company in connection with the tenant improvement allowance, a $0.4 million security deposit refund, and $0.2 million of legal and other related fees. In addition, the Landlord is required to facilitate the return and cancellation of the Company’s approximately $2.1 million letter of credit that had secured the Company’s obligations under the lease.

The Company determined that the Termination Agreement represents a nonrecognized subsequent event. Accordingly, the Company’s Condensed Consolidated Financial Statements as of and for the three and nine months ended September 30, 2026 have not been adjusted for the effects of the Termination Agreement. The Company does not expect the termination to have a material impact on its Consolidated Statements of Operations and Comprehensive Loss.