Quantum-si Incorporated · NASDAQ:QSI
Quantum-si — Investor Day (November 2025)
79 slides from Quantum-si's investor day presentation, Nov 19, 2025
Slide 1: Quantum Si Investor & Analyst Day
Quantum Si Investor & Analyst Day November 19, 2025 1
Slide 2: Investor Day Agenda
Investor Day Agenda Jeff Hawkins, CEO Tackling the Complexity of the Proteome 10:00–10:10 AM Proteus Program Update and Long-term Technology Todd Rearick, CTO 10:10–10:40 AM Roadmap John Vieceli, CPO The Path to Detecting All 20 Amino Acids 10:40–11:05 AM Brian Reed, Post-translational Modification
Slide 3: Proteins Are the Core of Biological Discoveries Across Many End Markets
Proteins Are the Core of Biological Discoveries Across Many End Markets Pharma + Academic Agriculture Industrial Biotech Research Clinical Translational Defense Research Diagnostics 3
Slide 4: Proteome Complexity
Proteome Complexity PROTEOME >1,000,000 PROTEOFORMS Post-translational Modifications TRANSCRIPTOME GENOME Alternative ~100,000 TRANSCRIPTS Promoters ~20–25,000 GENES Alternative splicing mRNA editing 4
Slide 5: The Study of Proteoforms Extends to Many Disease Areas and Thousands of Unique Proteins
The Study of Proteoforms Extends to Many Disease Areas and Thousands of Unique Proteins Affinity-based methods cannot scale to this complexity Complete coverage of the proteome would require hundreds of thousands or more unique, site- specific affinity reagents Only single-molecule protein sequencin
Slide 6: Proteoforms Are Not Limited to a Single PTM Type
Proteoforms Are Not Limited to a Single PTM Type They are far more diverse, even within a single protein Brains 0N3R 1N3R, 0N4R 1N4R Tau Immunoprecipitation Intact Tau isoforms/proteoforms Source: J. Proteome Res. 2025, 24, 6, 2916–2925 6
Slide 7: Proteoforms Also Include Single Amino Acid Variants
Proteoforms Also Include Single Amino Acid Variants, Which Can Be Critical to Understanding Disease Protein sequence Healthy Pro Glu Glu Variant Sickle Cell Disease Pro Val Glu Adapted from Ramadas N and Sparkenbaugh EM (2023). The APC-EPCR-PAR1 axis in sickle cell disease. Front. Med. 10:1141020. 7
Slide 8: Specialized Platforms With High Capital Costs Limit Adoption Outside of Core Labs
Specialized Platforms With High Capital Costs Limit Adoption Outside of Core Labs in Proteomics Many specialized platforms needed to fully interrogate the proteome Technical tradeoffs when selecting between the breadth of protein coverage and depth of insights High capital costs with the top end ins
Slide 9: Moving Beyond the Core Lab: Proteus Will Enable Deep Protein Analysis
Moving Beyond the Core Lab: Proteus Will Enable Deep Protein Analysis and Accelerate the Field of Proteomics Single-molecule protein sequencing will be the most versatile technology in proteomics — single AA variants, broad PTM coverage, and protein-agnostic Automation simplifies laboratory workflow
Slide 10: Themes of Today's Presentations
Themes of Today’s Presentations Proteus performance The path to detecting A diverse set of tools to Road to Proteus launch data and long-term all 20 amino acids enable generalizable and 2026 milestones technology roadmap PTM analysis 10
Slide 11: Proteus Program Update
QUANTUM SI Proteus™ Program Update
Slide 12: Proteus Next-generation Architecture
Proteus Next-generation Architecture Platinum® Pro + 2M Chip • Integrated semiconductor consumable • Benchtop instrument with manual workflow Proteus + KinetIQ Array • Simple, passive consumable • Benchtop instrument with imaging system • Workflow automation 12
Slide 13: KinetIQ Array
KinetIQ Array Simple, passive consumable • Low-cost fused silica die • 80M wells per device • Architecture scales to billions of wells Simple packaging • Inexpensive plastic assembly • Four flow cells, each with 20M wells • Features to support automation 13
Slide 14: Proteus Instrument
Proteus Instrument Liquid handling Optical module • Full workflow automation • High-performance custom • More advanced workflows, optical design deeper insights • High resolution and large field of view • Supports simple passive consumable 14
Slide 15: Proteus Program Status
Proteus Program Status Key technical risks retired or substantially reduced Critical system components matured through several prototypes Integrated system design complete — building first systems now 15
Slide 16: Sequencing Workflow Automation is More Reproducible Than Current Manual Workflow
Sequencing Workflow Automation is More Reproducible Than Current Manual Workflow Integrated System Liquid Handling Prototype Liquid Handling Subsystem Data Automated vs manual workflow alignments • Same architecture as integrated product design • Entire sequencing workflow fully automated 16
Slide 17: KinetIQ Array Fabrication and Post-processing Processes are Established
KinetIQ Array Fabrication and Post-processing Processes are Established Well structure optimized Product intent die size + geometry Wafer fabrication process established Wafer-scale post-processing Efficient packaging process 17
Slide 18: Data from Prototype Imaging System and New Dyes Validates Transition to Color Ratio
Data from Prototype Imaging System and New Dyes Fully Validates Transition from Lifetime to Color Ratio Fully Functional Imaging System Proven Color Channel Detection • Same architecture 450 4Cy3B • New color-space dye set as product design 400 4ATR6G • Demonstrated up to 8 dyes 350 • Commercial off
Slide 19: Successful Dynamic Sequencing Runs Completed in Q3
Successful Dynamic Sequencing Runs Completed in Q3 Sl17_V_APOE4(244–263)—LEE: 325 alignments 0.89 0.13 0.5 1.5 1.07 8.15 6.24 0.24 0.53 0.71 0.86 0.71 0.33 0.28 1.52 1.07 0.49 0.24 0.28 L E E Q A Q Q I R L Q A E A F Q A R L 87.4% 4.3% 65.2% 72.3% 96.3% 67.1% 30.2% 69.2% 71.4% 70.2% 50.2% 57.8% 19.7%
Slide 20: Proteus Has Superior Sequencing Output Per Well Compared to Platinum
Proteus Has Superior Sequencing Output Per Well Compared to Platinum Alignments per well (normalized to Platinum) Long-read fraction (normalized to Platinum) Proteus routinely produces more Proteus produces more long alignments with the same number of wells alignments compared to Platinum 20
Slide 21: Proteus Consistently Sequences Deep into Peptides
Proteus Consistently Sequences Deep into Peptides Sl19_V_IL6(87–120)—IIT: 439 alignments I I T G L L E F E V Y L E Y L Q N R F E S S E E Q A R A V Q M S 89.7% 94.3% 5.5% 88.2% 94.5% 76.8% 92.5% 90.7% 1.6% 85.2% 90.9% 75.4% 71.1% 63.3% 72.2% 30.1% 42.4% 59.0% 2.3% 0.7% 1.6% 1.4% 3.2% 3.2% 1.4% 0.2% 0
Slide 22: Proteus Has Superior SNR and Short Pulse Detection Compared to Platinum
Proteus Has Superior SNR and Short Pulse Detection Compared to Platinum Average SNR per wells Platinum Proteus Better SNR • More high-quality alignments • Better accuracy • More sensitive for PTMs and variants SNR Platinum More sensitive short pulse detection L Q A Q N Q W L Q D M • Increased mo
Slide 23: Proteus Sequencing Performance is on Track to Far Exceed Platinum at Launch
Proteus Sequencing Performance is on Track to Far Exceed Platinum at Launch Proteus data is already superior to Platinum data Data generated to date is without optimization Current algorithms | Current V4 binder set | Current cutters and chemistry Additional improvements expected before launch 23
Slide 24: Integrated System in Development
Integrated System in Development First Integrated System Expected 1Q26 • Full integration of imaging and workflow automation • Product-like consumables • Full field of view supporting 20M wells 24
Slide 25: Proteus Program Summary
Proteus Program Summary Transition to new architecture is proven — team is executing towards product launch for YE2026 Proteus architecture shows significant improvement over Platinum in the quantity and quality of sequencing output Platform launch is aligned with improvements in biochemistry and li
Slide 26: Long-term Technology Roadmap
Long-term Technology Roadmap 26
Slide 27: Proteus Architecture Supports Our Long-term Platform Roadmap Requirements
Proteus Architecture Supports Our Long-term Platform Roadmap Requirements Consumable architecture scales to billions of wells 10× scaling from assay Proteus 2.0 (up to 10B) improvements alone Future instruments capable of up to 10B reads Proteus Plus (up to 320M) Proteus (80M+) 27
Slide 28: Super Poisson Loading Increases Sequencing Output per Run by Approximately 3×
Super Poisson Loading Increases Sequencing Output per Run by Approximately 3× Poisson Loading • Peptides randomly loaded into wells • Maximum single-molecule loading ~36% • 64% of wells are empty or multiply-loaded Super Poisson Loading • Peptides are loaded in a way that prevents multiple loading •
Slide 29: Faster Sequencing Roadmap + Field Upgrades Could Drive Output Up to 320M
Faster Sequencing Roadmap + Field Upgrades Could Drive Output Up to 320M and Increase Samples per Run 5hr 2.5hr Proteus (80M) 160M 320M Proteus Plus (up to 320M) Sequencing time reductions allow more chips to be run in same timeframe as original 80M Upgrade to drawer/stage and consumable to increase
Slide 30: The Path to Billions of Reads Requires Controlled Cutting
The Path to Billions of Reads Requires Controlled Cutting Current Sequencing Chemistry Cutting happens randomly Residue duration is not uniform Time/residue is slower on average Controlled cutting would define the amino acid boundaries + enable a scanning system 30
Slide 31: We Have Successfully Demonstrated a Controlled Cleavage Version of Our Sequencing Chemistry
We Have Successfully Demonstrated a Controlled Cleavage Version of Our Sequencing Chemistry Controlled Cleavage Chemistry Enables scanning system Amino acid boundaries are known Residue duration is controlled and uniform Time/residue is much faster on average Defined Cutting Points 31
Slide 32: Combining Controlled Cleavage with High-speed Scanning Scales to Billions of Reads
Combining Controlled Cleavage with High-speed Scanning Scales the Architecture to Billions of Reads Proteus 2.0 can incorporate high-speed scanning and microfluidic delivery system Scanning system enables billions of reads Multiple imaging locations within one flow cell Efficient usage of device are
Slide 33: The Path to Detecting all Amino Acids
The Path to Detecting all 20 Amino Acids John Vieceli, Chief Product Officer November 19, 2025 33
Slide 34: Vision
Vision Develop a set of N-terminal amino acid recognizers for twenty canonical amino acids on Proteus 34
Slide 35: Recognizer Roadmap
QUANTUM SI Recognizer Roadmap
Slide 36: Sequencing Technology Overview
Sequencing Technology Overview Recognizers bind amino Recognition events acids in sequence produce kinetic signatures Kinetic signature plot 0.24s 3.23s 0.23s 0.97s Excitation ‘R’ Sequenced ‘L’ Sequenced ‘I’ Sequenced ‘F’ Sequenced R L I F 0 100 200 300 400 500 600 TIME (min) 36
Slide 37: Amino Acid Recognizers in Sequencing Kit V4
Amino Acid Recognizers in Sequencing Kit V4 Recognition for 14 of 20 amino acids using 6 recognizers FYW LIV R GAS NQ DE 37
Slide 38: Software Improvements Enable More Amino Acids
Software Improvements Enable More Amino Acids Q4 software release with Library Prep Kit V3 will increase to 15 amino acids FYW LIV R GAS NQM DE Peptide from L Q D A A V Y R M I Programmed Death-Ligand 1 C Peptide from Q L W F F N S M S Hepatocyte Growth Factor C P 38
Slide 39: Path to 20 Amino Acids with 8 Recognizers
Path to 20 Amino Acids with 8 Recognizers Detection of 18 amino acids demonstrated with campaigns for C and T underway FYW LIV RHK GA NQMC DE P TS LN Ⓗ V A V F A Ⓚ LA F A Ⓟ SNI F L 39
Slide 40: Recognizer Roadmap Supported on Proteus
Recognizer Roadmap Supported on Proteus Intensity and color ratio space supports 8+ dyes 450 4Cy3B Eight dyes have been demonstrated 400 4ATR6G on Proteus prototype system 350 4GGN C6C INTENSITY 300 Additional dye space available 4C53ONS 250 if necessary 200 150 3BGN FRET C2C 0 0.1 0.2 0.3 0.4 0.5 0
Slide 41: Recognizer Development Pipeline
Recognizer Development Pipeline
Slide 42: Recognizer Evolutionary Tree
Recognizer Evolutionary Tree 6 recognizers in Sequencing Kit V4 were derived from 4 starting proteins FYW2 FYW1 FYW1 FYW A. Tumefaciens | ClpS2 FYW1 LIV5 LIV4 LIV4 LIV1 LIV2 LIV3 LIV4 LIV6 LIV T. Elongatus | ClpS1 R3 R2 R2 QSI recognizers R1 R2 R4 R K. marxinus | UBR1 protected by 27 granted P1 pate
Slide 43: Quantum-Si N-terminal Amino Acid Recognizer Data
Quantum-Si N-terminal Amino Acid Recognizer Data Binding Data Structural Data Kinetic Data ~107 ~3,500 ~800 ~40 ~100 ~300 Labeled amino acid sequence data for binding N-terminal amino acids AI model refinement Predicted N-terminal amino acid binder 43
Slide 44: Protein Databank Mining for N-terminal Binders
Protein Databank Mining for N-terminal Binders Used for scaffold generation and model training N-terminal binding 287.848k interactions Ordered and complete 238.674k atomic representation Exposed 71.214k Single receptor 15.479k High-quality events 7,588 44
Slide 45: AI Model Refinement Enabled By Academia and Industry
AI Model Refinement Enabled By Academia and Industry Ligand message- Evolutionary GPU hardware passing neural network scale modeling acceleration 45
Slide 46: 4× Scale-up of Recognizer Development Pipeline
4× Scale-up of Recognizer Development Pipeline Utilize AI, rational, and combinatorial design approaches to generate candidates for screening pipeline Learning to feed designs Spectral analyzer Expression Combinatorial Dye label AI design Validation Production Rational design Bulk kinetics Week 1 We
Slide 47: X-ray Crystallography with Combinatorial and AI Strategies Yielded the GAS Recognizer
X-ray Crystallography with Combinatorial and AI Strategies Yielded the GAS Recognizer Crystal structure of NQ Several modifications in the recognizer with GAKL peptide pocket lead to G, A, and S binding, while not allowing for N and Q Info from combinatorial screening + AI 47
Slide 48: Proline Recognizer from AI and Combinatorial Methods
Proline Recognizer from AI and Combinatorial Methods Parent protein P Single mutant knockouts I P/I BINDING RATIO AMINO ACID POSITION 18 mutations 48
Slide 49: Summary of the Path to Twenty Amino Acids
Summary of the Path to Twenty Amino Acids Current recognizer pipeline has candidates to go from 14 amino acids with Sequencing Kit V4 to 18 at Proteus launch in 2026 Recognizer development program is being scaled 4× to achieve detection of all canonical amino acids in 2026 and release on Proteus in
Slide 50: PTM Analysis Solutions
PTM Analysis Solutions Brian Reed, PhD Head of Research 50
Slide 51: Agenda
Agenda PTM Solutions on Proteus 1 Advantages of single-molecule detection for PTMs 2 Broad access to PTMs on Proteus 3 PTM applications on the path to Proteus launch 51
Slide 52: PTMs and Proteoforms are the Next Frontier in Human Health
PTMs and Proteoforms are the Next Frontier in Human Health Palmitoylation A post-translational modification (PTM) is a Acetylation (Lys) AC (Cys) chemical change to an amino acid made after a Pal protein has been expressed. Su Phosphorylation (Ser/Thr/Tyr) P Sumoylation There are hundreds of differe
Slide 53: Challenge to Detecting PTMs With Existing Technologies
Challenge to Detecting PTMs With Existing Technologies Mass spectrometry Affinity-based platforms • Quantification difficult • Detect proteins but provide no • Ambiguity in modification site assignment proteoform information • Multi-site combinations extremely challenging OR • Workflow and analytica
Slide 54: Advantages of Single-molecule Detection for PTMs
Advantages of Single-molecule Detection for PTMs • Quantitation straightforward due to direct counting of molecules • Direct PTM site identification • Access to multi-site PTM combinations • Simple workflows for broad PTM proteome coverage; clinical compatibility • Universal PTM detection reagents a
Slide 55: Single-molecule Detection Enables Broad PTM Coverage
Single-molecule Detection Enables Broad PTM Coverage NGPS unlocks broad and universal access to PTMs with three complimentary approaches | Can be used in combination to address the most challenging needs in PTM detection Kinetics Pre-recognition Direct NAA detection PTM detected via kinetic PTM dete
Slide 56: Kinetic Detection of PTMs
Kinetic Detection of PTMs • Kinetic response to PTMs is a universal feature of NAA recognizers—when the chemical makeup of the peptide changes, the kinetics change. No extra reagents or processing steps needed • Examples: phospho-, methyl-, acetyl-, oxidation, citrullination • Customers are using to
Slide 57: Pre-recognition of PTMs
Pre-recognition of PTMs • PTM detection at any position regardless of peptide length • Parallel detection of multiple PTMs • E.g., Pan-phospho kit: Comprehensive detection of pS/pT/pY in one assay • Extreme sensitivity to PTM stoichiometry due to the clear pulsing pattern from PTM recognition 57
Slide 58: Direct N-terminal Detection of PTMs
Direct N-terminal Detection of PTMs Direct NAA detection • N-terminal PTM recognizer included in sequencing assay • Can be standard NAA recognizer or custom • Enables reference-free/de novo PTM discovery • Suitable for very complex sequence contexts and multisite PTM/variant arrangements 58
Slide 59: Kinetics: Influence of Downstream pY on NAA Recognizers
Kinetics: Influence of Downstream pY on NAA Recognizers Unmodified peptide How pY influences recognizer Used to detect tropomyosin kinetics in this peptide proteoforms • R pulse duration decreases from 1.3 to 0.5 sec. • L pulse duration increases from 2.5 to 3.5 sec. • Y is no longer recognized R L
Slide 60: Kinetics: Influence of Citrulline on NAA Recognizers
Kinetics: Influence of Citrulline on NAA Recognizers Arginine citrullination is challenging to detect by mass spec because of the negligible increase in mass (0.984 Da) Unmodified peptide PD (s) Arginine (R) 10 How citrulline influences FLR recognizer kinetics in this peptide 5 FLCit • F pulse durat
Slide 61: Kinetics: Multiple Kinetic Parameters Inform PTM Detection
Kinetics: Multiple Kinetic Parameters Inform PTM Detection Arginine (R) Citrulline (Cit) Citrulline and other PTMs influence multiple kinetic parameters Pulse duration (s): • Pulse duration: the lifetime of the recognizer-NAA bound state 0.48 1↑ • Interpulse duration: the time between recognizer bin
Slide 62: Pre-recognition: pY Detection at Any Peptide Location
Pre-recognition: pY Detection at Any Peptide Location An anti-phosphotyrosine antibody detects phosphotyrosine at any peptide location — N-terminal, internal, and C-terminal linker adjacent — independent of sequence context pY recognition Sequencing N-terminal pY Internal pY Y Internal pY pY adjacen
Slide 63: Pre-recognition: Carna Biosciences Kinase Panel
Pre-recognition: Carna Biosciences Kinase Panel Phosphorylation is a key determinant of activity for protein kinases used in drug discovery applications | Pre-recognition identifies phosphotyrosine in protein-tyrosine kinase 2-beta (PYK2B) and other important kinases pY recognition Sequencing Analys
Slide 64: Direct NAA Detection: Methionine Oxidation
Direct NAA Detection: Methionine Oxidation The NQM recognizer directly detects N-terminal methionine sulfoxide at position Met91 in IKBA NF-kappa-B inhibitor alpha (IKBA) Pulse duration distinguishes the modified and unmodified forms of methionine Methionine sulfoxide Unmodified methionine: PD = 0.3
Slide 65: We Have a Clear Path to Broad PTM Coverage on Proteus
We Have a Clear Path to Broad PTM Coverage on Proteus Recognizer Higher output Artificial PTM access with development on Proteus intelligence three methods Recognizers for all 20 Enables deeper and more For data analysis to fully Three complimentary amino acids will ensure sensitive PTM detection ex
Slide 66: The Road to Proteus Launch
QUANTUM SI The Road to Proteus € Launch
Slide 67: From Platinum to Proteus — Market Learnings Inform Commercial Strategy
From Platinum to Proteus — Market Learnings Inform Proteus Requirements and Commercial Strategy General technology first; Defined applications first; defined applications second general technology second Sample prep-agnostic Sample-to-report workflows for high-value applications Broad marketing to a
Slide 68: The Customer Data is Clear
The Customer Data is Clear Researchers need a breadth of capabilities to answer their biological questions Number of PTMs Required Number of Unique Applications More than 50 detailed study proposals submitted by prospective customers >50% require three or more One Two Three or more types of protein
Slide 69: A Look Inside an Academic Medical Center
A Look Inside an Academic Medical Center Academic Medical Center Basic Research Lab Core Lab Translational Lab Clinical Lab • Wide range of • Many technologies in • Targeted applications; • Defined application application interests use in one lab many involve PTMs content; sample-to- report workflow
Slide 70: Platinum Case Study — The Academic Medical Center
Platinum Case Study — The Academic Medical Center Academic Medical Center Basic Research Lab Core Lab Translational Lab Clinical Lab Good value prop but Limited to reflex testing Adoption limited by Not accessible with most users are low- downstream of current technology Platinum Pro utilization mas
Slide 71: Increased Sequencing Output and Lower Costs of the Nanowell Array
The Increased Sequencing Output and Lower Costs of the Nanowell Array is Broadly Enabling More samples per run with 40× the output per consumable compared to Platinum Pro Deep analysis of a single sample to address complex mixtures or rare events like variants or PTMs Multiplexing samples to achieve
Slide 72: Accelerating Core Sequencing Technology and Analytics to Unlock High-value Applications
Accelerating the Core Sequencing Technology and Analytics to Unlock the Highest-value Applications Robust PTM detection Sequencing of variable and multi-PTM profiling regions of antibodies Single-amino acid Biothreat detection variant detection and surveillance 72
Slide 73: Proteus Automation Greatly Simplifies the Sequencing Workflow
Proteus Automation Greatly Simplifies the Sequencing Workflow and Makes New Lab Startup Even Easier Over 30 individual reagent tubes A single reagent module per run to handle to process four samples — simply unbox and load Over 100 pipetting steps per sample Pipette your sample(s) into the cartridge
Slide 74: Building a Partner Ecosystem to Accelerate Application Development
Building a Partner Ecosystem to Accelerate Application Development + Deliver Sample-to-report Workflows Application Sample Prep Applications of Development + Enrichment AI for Data Analysis 74
Slide 75: New Industry Partnerships in PTMs and Ultra-low-abundance Protein Panels
New Industry Partnerships in PTMs and Ultra-low- abundance Protein Panels • Carna Biosciences is a leading provider of • Siena Quant is a SISCAPA Holdings assay-grade kinase proteins to biopharma for Company — experts in the field of sample drug discovery and profiling enrichment for proteomics • Ca
Slide 76: Proteus Will Increase the Depth of Penetration in Academic Medical Centers
Proteus Will Increase the Depth of Penetration in Academic Medical Centers Compared to Platinum Academic Medical Center Basic Research Lab Core Lab Translational Lab Clinical Lab Single-molecule protein High-value application Expanded PTM capabilities Automation + sample-to- sequencing will remain a
Slide 77: Proteus Will Enable Single-molecule Protein Sequencing Across a Broad Range of End Markets
Proteus Will Enable Single-molecule Protein Sequencing Across a Broad Range of End Markets Pharma + Academic Agriculture Industrial Biotech Research Clinical Translational Defense Research Diagnostics 77
Slide 78: Milestones on the Path to Proteus Launch in 2026
Milestones on the Path to Proteus Launch in 2026 End-to-end sequencing Sequencing on Fully integrated on fully integrated systems Internal Launch Proteus systems delivered (Q2) V&V (Q4) prototype and operational (Q4) (Q1) External customer collaborations initiated (summer 2026) 4Q25 1Q26 2Q26 3Q26 4
Slide 79: QSI is Well-positioned to Build Upon Our First-to-market Advantage
QSI is Well-positioned to Build Upon Our First-to-market Advantage and Extend Our Leadership into the Future Grow user base with Execute on Build a partner Extend our technology Platinum Pro and development roadmap ecosystem to lead through best-in- develop the market for to deliver a compelling acc