Corporate Presentation

Forward Looking Statements This presentation includes "forward-looking statements" within the meaning of the "safe harbor" provisions of the United States Private Securities Litigation Reform Act of 1995. The actual results of Quantum-Si Incorporated (the “Company”) may differ from its expectations, estimates, and projections and, consequently, you should not rely on these forward-looking statements as predictions of future events. Words such as "expect," "estimate," "project," "budget," "forecast," "anticipate," "intend," "plan," "may," "will," "could," "should," "believes," "predicts," "potential," "continue," and similar expressions (or the negative versions of such words or expressions) are intended to identify such forward-looking statements. These forward-looking statements include, without limitation, the Company's expectations with respect to future performance and development and commercialization of products and services, its anticipated cash runway and its financial guidance for the full year 2024. These forward-looking statements involve significant risks and uncertainties that could cause the actual results to differ materially from those discussed in the forward-looking statements. Most of these factors are outside the Company's control and are difficult to predict. Factors that may cause such differences include, but are not limited to: the inability to maintain the listing of the Company's Class A common stock on The Nasdaq Stock Market; the ability of the Company to grow and manage growth profitably and retain its key employees; the Company’s ongoing leadership transitions; changes in applicable laws or regulations; the ability of the Company to raise financing in the future; the success, cost and timing of the Company's product development and commercialization activities; the commercialization and adoption of the Company’s existing products and the success of any product the Company may offer in the future; the potential attributes and benefits of the Company’s commercialized Platinum® protein sequencing instrument and kits and the Company’s other products once commercialized; the Company's ability to obtain and maintain regulatory approval for its products, and any related restrictions and limitations of any approved product; the Company's ability to identify, in-license or acquire additional technology; the Company's ability to maintain its existing lease, license, manufacture and supply agreements; the Company's ability to compete with other companies currently marketing or engaged in the development or commercialization of products and services that serve customers engaged in proteomic analysis, many of which have greater financial and marketing resources than the Company; the size and growth potential of the markets for the Company's products and services, and its ability to serve those markets once commercialized, either alone or in partnership with others; the Company's estimates regarding future expenses, future revenue, capital requirements and needs for additional financing; the Company's financial performance; and other risks and uncertainties described under "Risk Factors" in the Company’s most recent Annual Report on Form 10-K, and in the Company's other filings with the SEC. The Company cautions that the foregoing list of factors is not exclusive. The Company cautions readers not to place undue reliance upon any forward-looking statements, which speak only as of the date made. The Company does not undertake or accept any obligation or undertaking to release publicly any updates or revisions to any forward-looking statements to reflect any change in its expectations or any change in events, conditions, or circumstances on which any such statement is based. Non-GAAP Financial Measures This presentation includes certain non-GAAP financial measures including “adjusted total operating expenses”. Please see Exhibit 99.2 to the Company’s Current Report on Form 8-K filed with the SEC on August 7, 2024, for further discussion of the Company’s use of non-GAAP financial measures. Disclaimer and Other Information

Quantum-Si: The Protein Sequencing Company™ Founded in 2013; NASDAQ (QSI) since June 2021 Experienced team from life sciences leaders including Illumina, PacBio, and Ion Torrent Launched the world’s first Next-Generation Protein Sequencing™ system, Platinum® in December 2022 Over 1,000 owned and licensed patents and applications issued or pending Strong financial position — cash runway expected into 2026

The World’s First Next-Generation Protein Sequencer™ Unmatched Accessibility List Price <$100K Automated data analysis Addresses gaps in existing genomics and proteomics research workflows Proprietary Technology Kinetic signatures enable single amino acid resolution Single-molecule sensitivity Extensible beyond protein sequencing Deeper Insights Protein variants Post-translational modifications Unbiased protein identification

Company Key Updates 2023 Highlights Launched Platinum® in Dec 2022 2024 Guidance Launched V2 sequencing kit in 1Q24 Successfully executed controlled launch, generating $1.1M in revenue Full Commercial Launch initiated 1Q24 Built a world-class leadership team Appointed independent Chairman of BOD Transformed organization from research into commercial phase Launched V3 sequencing kit 3Q24 Enhanced Board of Directors with three new independent directors New Library Prep and Barcoding Kit YE24 Lowered Adjusted OpEx Y/Y Full Year Revenue: $3.7M–4.2M Adjusted OpEx: $103M or less Cash usage: $100M or less

Proteomics Is A Large And Growing Market Opportunity SVB Leerink Research, “Proteomics: The Next Frontier in Life Science Tools and Diagnostics,” September 28, 2021 DeciBio Consulting Evaluation, June 2020 $75B+ Proteomics Market1 Research $20B+ EmergingClinical $55B+ $8B+ Initial Target Market2 Identification $3B+ Expression + Quantification $3B+ Proteoforms+ PTMs $1.5B+ Identification $3B+ Expression + Quantification $3B+ Proteoforms+ PTMs $1.5B+

Proteins Are More Complex And Actionable Than DNA or RNA 1,000,000+ Proteoforms (Protein) 200,000 Sequences (RNA) 20,000 Genes (DNA) DNA is the blueprint but has limited actionability RNA is more actionable but does not tell the complete story Proteins are extraordinarily diverse and are the real time indicators of health and disease, making them the most actionable 7

Disease Progression Goes Beyond The Protein Level Human Proteoform Project https://www.science.org/doi/10.1126/sciadv.abk0734

Core Areas Of Proteomics Research Today HT Affinity Assays Mass Spec EdmanDegradation Western Blots + ELISA Samples: 100s–1,000s per study Proteins: 1000s per sample Resolution: Protein Protein Level Screening Samples: 10s–100s per study Proteins: <50 per sample Resolution: Amino acid; Single-molecule Focused and Deep Characterization

Deeper Insights With Unprecedented Accessibility High-throughput affinity-based assays Mass spec Edman degradation Western blots and ELISA DATA RICHNESS ACCESSIBILITY

The Quantum-Si Solution Sequence Platinum® sequences individual peptides and provides amino acid level resolution Prepare Library Preparation and Sequencing Kits contain everything you need to digest and functionalize proteins and sequence them on our proprietary semiconductor chip Analyze Our analysis software automatically delivers single-molecule level information about your proteins without the need for bioinformatics expertise

Sequence Proteins With Next-Generation Protein Sequencing Sequence Prepare Analyze

The Value of Deeper Insights With Next-Generation Protein Sequencing ProteinEngineering Engineering proteins for therapeutic, industrial, or environmental purposes AntibodyCharacterization Antibody validation isnecessary for research useand drug development DrugDiscovery Studying and screening drug candidates for downstream proteomic outcomes

Differentiating Disease Relevant Proteoforms with Next-Generation Protein SequencingDr. Gloria Sheynkman lab | Festival of Genomics, ASMS Presented at ASMS 2024 and Festival of Genomics 2024; publication in preparation Different TPM2 isoforms affect bone mineral density, impacting muscle and skeletal function Difficult to distinguish on mass spectrometry Platinum was successfully able to differentiate TPM2 isoforms Phe (F), Tyr (Y), Trp (W)

Next-Generation Protein Sequencing is Complementary to Mass Spec in PTM AnalysisDr. Neil Kelleher lab | ASMS Pyroglutamate (pE) is a disease-relevant PTM in neurological disease This PTM can also be produced by artifacts in Mass Spectrometry protocols, complicating analyses and producing false-negatives Next-Generation Protein Sequencing can accurately detect pE modified peptides following pE-aminopeptidase treatment Presented at ASMS 2024; publication in preparation

Platinum Complements And Enhances Current Proteomic and Genomic Workflows Immunoassays Uncover more than antibodies can with accurate protein identification and amino acid resolution MassSpectrometry Identify proteins with ease and gain deeper insights with single-molecule amino acid level resolution Next-GenSequencing Compliment genomic datasets with protein analysis and uncover direct protein-to-phenotype relationships InsourcingProtein Analysis Identify proteins and modifications without the need for expensive equipment, expertise,or infrastructure − + + − + +

Expanding Our Global Commercial Channels + Partnerships 2024 Commercialization Approach Direct Sales Force Presence Distributor Partner Presence

2024 Commercial Priorities Build Our Distribution Network Engage with leading life science tools distributors in select regions Expand Our Direct Team Expand direct sales and serviceteam in US and Western Europe Execute on Full Commercial Launch On-site demos to accelerate customer evaluation; Grow the installed base;Drive consumable usage New Product Launches Launched Version 2 kit to customersin February 2024; LaunchedVersion 3 kit in August 2024 Drive Awareness Through Data Posters/presentations at conferences,peer-review publications, webinars

Introducing the Version 3 Sequencing Kit Enhanced Insights The power of our single-amino acid resolution platform is amplified with the addition of Aspartic acid (D) recognition and improved performance of other recognizers Simplified Workflow Accelerating results with less hands-on time and AI-powered analysis tools for elevated protein insights making protein sequencing more accessible Progressive Innovation Our latest recognizer set expands access to protein characterization and amino acid variation to accelerate your next breakthrough

Delivering on the Innovation Roadmap to Continuously Expand Proteome Coverage

V3 Sequencing Kit Offers Increased Output and Value to Customers Amino Acids Sequenced per Chip More than 5.5-fold increase since V1 Cost per 1,000 Amino Acids More than 4.5-fold reduction in cost since V1

AUG 24 JAN 24 OCT 22 MAR 23 2H 24 DEC 22 BEYOND JUN 23 Innovation Pipeline is Robust and Accelerating Sequencing V1 V2 V3 V+ Instruments + Software UI/UX ProteinInference AI KineticDatabase V2 AI KineticDatabase V3 Library Prep V+ V1 V2

2024 Corporate Priorities Accelerate commercial adoption Full commercial launch; Direct and distribution model scale-up;Revenue of $3.7M–4.2M Deliver on our innovation roadmap V2 Kit launched in 1Q24; V3 Kit Launched in 3Q24;Innovation pipeline accelerating; library prep and barcoding kits by YE24 Preserve financial strength Guidance of adjusted OpEx of $103M or less;Cash usage of $100M or less

Q&A