SCHEDULE 13D/A 0001104659-21-083432 0001076352 XXXXXXXX LIVE 4 Class A common stock, par value $0.0001 per share, Class B common stock, par value $0.0001 per share 09/09/2025 false 0001816431 74765K105 Quantum-Si Inc

29 BUSINESS PARK DRIVE BRANFORD CT 06405

Jonathan M. Rothberg, Ph.D. (866) 688-7374 c/o Quantum-Si Incorporated 29 Business Park Drive Branford CT 06405 0001076352 ROTHBERG JONATHAN M PF X1 12085926 2190489 12085926 2190489 14276415 N 7.8 IN This Reporting Person's Table is for Class A common stock. Rows 7, 9 and 11 consists of (i) 2,568,443 shares of Class A common stock of Quantum-Si Incorporated (the ''Issuer'') held by Jonathan M. Rothberg, Ph.D., (ii) stock options to purchase 543,642 shares of Class A common stock of the Issuer which are exercisable within 60 days of September 9, 2025, held by Dr. Jonathan M. Rothberg and (iii) an aggregate of 8,973,841 shares of Class A common stock of the Issuer held by entities owned by trusts created for the benefit of Dr. Jonathan Rothberg's children, including shares of Class A common stock previously distributed from 2012 JMR Trust Common, LLC. Rows 8, 10 and 11 consists of (i) 1,917,067 shares of Class A common stock of the Issuer held by 23rd Century Capital LLC, and (ii) 273,422 shares of Class A common stock of the Issuer held by Dr. Jonathan Rothberg's spouse, Bonnie E. Gould Rothberg, M.D. Row 13 is calculated based on 182,557,698 shares of Class A common stock of the Issuer outstanding as of July 31, 2025. Y ROTHBERG JONATHAN M. PF X1 19937500 0 19937500 0 19937500 N 100 IN This Reporting Person's Table is for Class B common stock. Rows 7, 9 and 11 consists of (i) 17,943,750 shares of Class B common stock of the Issuer held by 4C Holdings I, LLC and (ii) 1,993,750 shares of Class B common stock of the Issuer held by 4C Holdings V, LLC. Row 13 is calculated based on 19,937,500 shares of Class B common stock of the Issuer outstanding as of July 31, 2025. Y 23rd Century Capital LLC PF DE 1917067 1917067 1917067 N 1.05 OO This Reporting Person's table is for Class A common stock. Row 13 is calculated based on 182,557,698 shares of Class A common stock of the Issuer outstanding as of July 31, 2025. Y 2012 JMR Trust Common, LLC PF DE 0 OO This Reporting Person's table is for Class A common stock. Row 13 is calculated based on 182,557,698 shares of Class A common stock of the Issuer outstanding as of July 31, 2025. Y 4C Holdings I, LLC PF DE 17943750 17943750 17943750 N 90 OO This Reporting Person's table is for Class B common stock. Row 13 is calculated based on 19,937,500 shares of Class B common stock of the Issuer outstanding as of July 31, 2025. Y 4C Holdings V, LLC PF DE 1993750 1993750 1993750 N 10 OO This Reporting Person's table is for Class B common stock. Row 13 is calculated based on 19,937,500 shares of Class B common stock of the Issuer outstanding as of July 31, 2025. Class A common stock, par value $0.0001 per share, Class B common stock, par value $0.0001 per share Quantum-Si Inc 29 BUSINESS PARK DRIVE BRANFORD CT 06405 Explanatory Note Amendment No. 4 to Schedule 13D ("Amendment No. 4") amends and supplements the Schedule 13D dated June 18, 2021, as amended by Amendment No. 1 filed on September 13, 2023, Amendment No. 2 filed on September 17, 2024 and Amendment No. 3 filed on December 31, 2024 (collectively, as amended, the "Schedule 13D") relating to the Class A common stock, par value $0.0001 per share ("Class A common stock"), and Class B common stock, par value $0.0001 per share, of Quantum-Si Incorporated, a Delaware corporation. Information reported in the Schedule 13D remains in effect except to the extent that it is amended, restated or superseded by information contained in this Amendment No. 4. Capitalized terms used but not defined herein have the meanings ascribed to them in the Schedule 13D. In connection with estate planning, entities owned by trusts created for the benefit of Dr. Jonathan Rothberg's children have entered into a trading plan pursuant to Rule 10b5-1 under the Securities Exchange Act of 1934, as amended (the "Plan"), a copy of which is attached hereto as Exhibit 5. Pursuant to the Plan, sales of up to 8,973,841 shares of Class A common stock may be effected during the plan sales period beginning following the cooling-off period contained in Rule 10b5-1(c) on January 14, 2026 and ending on January 14, 2027 in accordance with the terms and conditions of the Plan. The sale of shares of Class A common stock under the Plan is subject to minimum price parameters included in the Plan, and there is no assurance that any shares of Class A common stock will be sold under the Plan. Item 7 of the Schedule 13D is hereby amended by adding the following exhibit: 5. Rule 10b5-1 Trading Plan ROTHBERG JONATHAN M /s/ Jonathan M. Rothberg 09/11/2025 ROTHBERG JONATHAN M. /s/ Jonathan M. Rothberg 09/11/2025 23rd Century Capital LLC /s/ Jonathan M. Rothberg 09/11/2025 2012 JMR Trust Common, LLC /s/ Jonathan M. Rothberg 09/11/2025 4C Holdings I, LLC /s/ Jonathan M. Rothberg 09/11/2025 4C Holdings V, LLC /s/ Jonathan M. Rothberg 09/11/2025