Senior Scientist, Systems Integration

Quantum-Si • San Diego, CA

1d • $135,000 - $155,000

About The Position

Quantum-Si is seeking a Senior Systems Integration Scientist to drive integration, characterization, and troubleshooting for Proteus, its next-generation single-molecule protein sequencing platform. The role investigates performance across samples, reagents, surface chemistry, consumables, fluidics, instrumentation, and sequencing workflows. Through hands-on experimentation, statistical design, root-cause analysis, and system-level thinking, the scientist will improve product performance, reproducibility, robustness, and customer readiness.

The position leads system-level characterization and investigations, develops rigorous experimental methods, evaluates stability and customer-relevant workflows, and contributes evidence to verification, validation, reliability, risk assessments, and product decisions. The scientist works across scientific, engineering, quality, manufacturing, operations, and customer-facing teams, and documents findings and recommendations with technical rigor and traceability. Travel of up to 20 percent is required, including overnight and occasional international travel.

Requirements

• Ph.D. in biochemistry, chemistry, chemical engineering, biomedical engineering, bioengineering, molecular biology, materials science, biophysics, polymer science, analytical chemistry, or a related discipline with relevant 3–5 years of industry experience; or an M.S./B.S. with substantial equivalent industry experience.
• Strong scientific foundation in protein chemistry, biochemistry, analytical chemistry, surface chemistry, biomaterials, reagent formulation, molecular assays, biosensors, or chip-based assays.
• Demonstrated experience integrating or troubleshooting assays, reagents, samples, materials, consumables, or automated life-science instrumentation.
• Ability to lead structured root-cause investigations, develop hypotheses, design controlled experiments, interpret complex results, and make evidence-based technical recommendations involving biological, chemical, material, or instrument interactions.
• Experience with design of experiments and statistical analysis using JMP, Python, R, MATLAB, Minitab, or equivalent tools.
• Knowledge of sample and reagent stability, material compatibility, surface interactions, contamination controls, environmental robustness, or accelerated-stability testing.
• Experience developing experimental protocols, test methods, acceptance criteria, controls, and technical reports.
• Ability to analyze system-level datasets and relate scientific variables to integrated instrument or product performance.
• Hands-on laboratory experience with biological samples, reagents, consumables, prototype systems, and automated instrumentation.
• Ability to manage multiple workstreams independently and collaborate effectively across scientific and engineering teams.
• Strong technical communication skills and ability to explain complex scientific findings to multidisciplinary audiences.
• Detail-oriented, objective, and rigorous approach to experimentation, data interpretation, and documentation.
• Ability to travel up to 20 percent, including overnight and occasional international travel.
• Must be authorized to work in the United States; employment-based immigration sponsorship is not provided.

Nice To Haves

• Experience with proteomics, protein sequencing, next-generation sequencing, single-molecule detection, fluorescence-based detection, biosensors, sensor arrays, silicon photonics, or chip-based analytical platforms.
• Experience with protein immobilization, surface functionalization, nonspecific adsorption, biofunctional coatings, biomolecule-surface interactions, and evaluating plastics, foils, polymers, adhesives, elastomers, metals, or other materials that contact biological samples or reagents.
• Experience with reagent formulation, buffers, enzymes, proteins, peptides, labeling chemistries, stabilizers, preservatives, or other biologically active materials.
• Experience designing accelerated and real-time stability studies; investigating sample or reagent degradation, background, loss of activity, contamination, evaporation, and time-dependent performance changes; and establishing scientifically justified storage, handling, and operating-time recommendations.
• Experience with microfluidics, fluid handling, liquid handling, thermal workflows, incubation control, low-volume sample handling, or automated biological workflows.
• Experience using microscopy, fluorescence measurements, spectroscopy, imaging, surface-characterization methods, or other analytical techniques to investigate system-performance issues.
• Experience with verification and validation, product characterization, reliability testing, design controls, FMEA, CAPA, risk assessment, deviation investigations, commercialization, product transfer, manufacturing investigations, reliability growth, field issue resolution, or customer-facing technical escalations.
• Experience working under quality-system expectations, including good documentation practices, controlled protocols, issue tracking, and traceable technical decision-making.
• Familiarity with Jira, Confluence, requirements-management systems, laboratory information systems, or structured experimental-data repositories.
• Experience working in a start-up, rapidly evolving product-development organization, or cross-functional matrix environment.

Responsibilities

• Design and execute system-level studies to identify critical parameters, interaction effects, operating ranges, and sources of variability across samples, reagents, surface chemistry, consumables, materials, fluidics, instrument conditions, and sequencing workflows.
• Investigate surface and material interactions affecting sample loading, biomolecule immobilization, reagent activity, background, signal quality, and sequencing performance.
• Partner with Surface Chemistry and Consumables teams to characterize material compatibility, adsorption, contamination, surface variability, and manufacturing or environmental effects, and translate findings into product improvements.
• Design and execute on-board, off-board, accelerated, and stress studies to characterize sample and reagent stability under customer-relevant storage and operating conditions.
• Identify degradation mechanisms and establish scientifically supported storage, handling, hold-time, and operating recommendations while differentiating sample, reagent, consumable, chip, surface, and instrument effects.
• Design statistically rigorous experiments, including multifactor DOE, with appropriate controls and acceptance criteria to identify critical variables, interaction effects, failure thresholds, and optimal operating conditions.
• Analyze complex experimental and sequencing datasets using JMP, Python, R, MATLAB, or equivalent tools, and communicate performance trends, variability, scientific risk, conclusions, and recommendations.
• Lead cross-functional investigations with Surface Chemistry, Reagent Development, Applications, Consumables, Engineering, Software, Quality, Manufacturing, Operations, and Customer Success.
• Translate system-level observations into focused studies, integration strategies, and evidence-based conclusions.
• Develop reproducible experimental protocols, characterization plans, test methods, controls, acceptance criteria, analysis methods, and troubleshooting workflows.
• Design and execute verification and validation, characterization, robustness, reliability, and regression studies demonstrating that integrated performance meets system requirements.
• Investigate deviations, outliers, and emerging performance trends and contribute scientific evidence to risk assessments, failure-mode analyses, mitigations, and product decisions.
• Evaluate sequencing performance under customer-relevant samples, workflows, environmental conditions, timing, and operator interactions.
• Investigate field issues involving sample quality, reagent handling, consumables, surface chemistry, environmental exposure, or integrated workflows, and translate findings into practical product and troubleshooting recommendations.
• Author experimental plans, protocols, technical reports, investigation summaries, risk assessments, and scientifically justified recommendations with appropriate technical rigor and traceability.
• Communicate complex scientific findings, evidence, risks, decisions, and recommendations to technical teams, cross-functional stakeholders, and leadership.

Benefits

• Comprehensive medical, dental, and vision insurance coverage.
• Health Savings Account (HSA) and Flexible Spending Account (FSA) options, where applicable.
• Company-paid life and accidental death and dismemberment (AD&D) insurance.
• Short-term and long-term disability coverage.
• Employee Assistance Program (EAP) resources.
• Discretionary paid time off and company-paid holidays.
• Parental leave.
• 401(k) retirement savings plan with pre-tax and Roth contribution options.
• Eligible full-time employees may participate in the discretionary annual bonus program and may receive equity awards.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree