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 May 9, 2024 for further discussion of the Company’s use of non-GAAP financial measures. Disclaimer and Other Information

Quantum-Si: The Protein Sequencing CompanyTM 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 and pending Strong financial position - cash runway expected into 2026

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

Company Key Updates 2023 Highlights 2024 Guidance Launched Platinum® in Dec 2022 Successfully executed controlled launch generating $1.1M in revenue Built a world class leadership team Transformed organization from research into commercial phase Enhanced Board of Directors with three new independent directors Lowered Adjusted OpEx Y/Y Launched V2 Kit in 1Q24 Full Commercial Launch initiated at end of Q1 2024 Appointed independent Chairman of BOD Version 3 Kit targeting 3Q24 Full Year Revenue: $3.7M - $4.2M Adjusted OpEx: $103M or less Cash Usage: $100M or less Cash Runway expected into 2026

$75B+ Proteomics Market1 $8B+ Initial Target Market2 Proteomics Is A Large And Growing Market Opportunity Research $20B+ Emerging Clinical $55B+ Identification $3B+ Expression & Quantification $3B+ Proteoforms & PTM’s $1.5B+ 1. SVB Leerink Research, “Proteomics: The Next Frontier in Life Science Tools and Diagnostics”, September 28, 2021 2. DeciBio Consulting Evaluation, June 2020

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

Core Areas Of Proteomics Research Today Population Screening Samples: 100’s-1000’s per study Proteins: 1000’s per sample Resolution: Protein Deep Characterization Samples: 10’s-100’s per study Proteins: <50 per sample Resolution: Amino acid; Single-molecule Mass Spec HT Affinity Assays Edman Degradation Western Blots & ELISA

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

Deeper Insights With Unprecedented Accessibility Mass Spec High Throughput Affinity Based Assays Edman Degradation Western Blots and ELISA Data Richness Accessibility

Library Preparation and Sequencing Kits contain everything you need to digest and functionalize proteins and sequence them on our proprietary semiconductor chip The Quantum-Si Solution Prepare Sequence Analyze Platinum® sequences individual peptides and provides amino acid level resolution 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 Protein Engineering Antibody Characterization Protein-Protein Interactions Disease Relevance Who Academics, Biopharma, Industry Academics, Biopharma, Industry Academics, Biopharma Academics, Biopharma What Engineering proteins for therapeutic, industrial or environmental purposes Antibody validation is necessary for research use and drug development Studying protein interactions for purposed of drug ID/characterization Studying variants of proteins and how that affect disease outcome Why Direct confirmation of which protein sequence correlates to desired function Ensure protein performs poorly in required application Antibody sequence changes can alter performance and reproducibility of results Having sequence specific information can shorten research and development times and reduce costs. 3D structure of proteins is based on the protein sequence and determines how proteins interact Changes at the amino acid sequence level may alter the function or regulation of biological pathways Mutations or changes in amino acid sequence are usually spontaneous and not present in all cells Understanding mutations associated with disease may provide more precise treatment options

Compliment genomic datasets with protein analysis and uncover direct protein to phenotype relationships Platinum® Complements And Enhances Current Proteomic and Genomic Workflows Next-Gen Sequencing Immunoassays Mass Spectrometry Uncover more than antibodies can with accurate protein identification and amino acid resolution Identify proteins with ease and gain deeper insights with single molecule, amino acid level resolution Insourcing Protein Analysis Identify proteins and modifications with out the need for expensive equipment, infrastructure or expertise

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

2024 Commercial Priorities Accelerate the Purchase Process On-site demos allow customers to evaluate the technology in their own lab Build Our Distribution Network Engage with leading life science tools distributors in select regions – expand network upon proving out model Execute on Full Commercial Launch Expand team in direct markets; Grow the installed base; Drive consumable usage Drive Awareness Through Data Posters/presentations at conferences, peer-review publications, webinars New Product Launches Deploy the Version 2 kit to customers in 1Q; Launch Version 3 kit targeting 3Q24

Product Enhancements Delivered With The Version 2 Kit And New Software Increased proteome coverage with an additional amino acid recognizer Increased output and improved reproducibility Confidently identify proteins with advanced analytical and inference tools Enhanced flexibility with various sample inputs

Significant Improvement In Product Performance Using The Version 2 Kit 1K Amino Acids per Chip IL4 IL6 CDNF PDL1 Version 1 Kit Version 2 Kit Increase in Amino Acids Sequenced Increase in Peptides Identified Number of Identified Peptides IL4 IL6 CDNF PDL1 Version 1 Kit Version 2 Kit +4X +2X +3X +5X 6 6 5 5 6 4 3 3

Version 2 Kit Demonstrates High Reproducibility Providing Customers More Flexibility In Study Design Performance With Proteins # of Alignments Right Side of Chip # of Alignments Left Side of Chip Single Peptide 10 Peptide Barcodes Performance With Peptides # of Alignments Left Side of Chip (log) IL4 HSA VIME CDNF # of Alignments Right Side of Chip (log) AKT1 H4 PDL1 IL6 FGF2

Version 2 Kit Delivers An Approximate 3-Fold Reduction In Cost Per 1,000 Amino Acids Amino Acids per Chip (1K) Version 1 Kit Version 2 Kit Cost per 1,000 Amino Acids 528K 154K

Our Innovation Pipeline Is Accelerating Completed R&D Re-alignment Announce V2 Kit targeting 1Q24 Launch August 2023 V2 Sequencing Kit Launched February 2024 Innovation roadmap continues towards true de-novo sequencing 2026+ Developing new innovations across library prep, sequencing, instruments and applications 2H24-2025 Announced V3 Kit targeting 3Q24 Full Commercial Launch initiated at end of 1Q24 Innovation pipeline in library prep and instrumentation 4Q2023 Earnings Call Update 3Q24E Estimated V3 Sequencing Kit Launch Platinum® introduced to the market December 2022

2024 Corporate Priorities Accelerate commercial adoption Deliver on our innovation roadmap Preserve financial strength Full commercial launch; Direct and distribution model scale up; Revenue of $3.7M - $4.2M V2 Kit Launched in February 24; V3 Kit Launch Targeting 3Q24; Innovation pipeline accelerating Guidance of Adjusted OpEx of $103M or less; Cash Usage of $100M or less

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