Senior Scientist, Systems Integration

Quantum-Si•San Diego, CA

22h

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 improves product performance, reproducibility, robustness, and customer readiness. The scientist designs system-level characterization, stability, verification, validation, reliability, regression, and customer-relevant workflow studies. The work includes investigating surface and material interactions, sample and reagent stability, sources of variability, deviations, field issues, and failure mechanisms. The role develops rigorous methods, protocols, controls, and acceptance criteria; analyzes complex datasets; and translates evidence into product improvements and practical recommendations. This position leads cross-functional scientific investigations with teams across research, engineering, quality, manufacturing, operations, and customer success. It also requires technical documentation and clear communication of findings, risks, and recommendations to multidisciplinary teams and leadership. Travel of up to 20 percent is required, including overnight and occasional international travel.

Requirements

Ph.D. in a relevant discipline with 3–5 years of industry experience, or an M.S. or 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 evaluation of 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 and investigating sample or reagent degradation, background, loss of activity, contamination, evaporation, or time-dependent performance changes.
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 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 compatibility, adsorption, contamination, variability, and manufacturing or environmental effects.
Design 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.
Design statistically rigorous experiments, including multifactor design of experiments, with appropriate controls and acceptance criteria; analyze complex experimental and sequencing datasets and communicate trends, variability, risks, conclusions, and recommendations.
Lead cross-functional investigations and translate system-level observations into focused studies, integration strategies, and evidence-based conclusions.
Develop reproducible 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 to demonstrate 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 and provide practical product and troubleshooting recommendations.
Author experimental plans, protocols, technical reports, investigation summaries, risk assessments, and scientifically justified recommendations with appropriate rigor and traceability.
Communicate scientific findings, evidence, risks, decisions, and recommendations to technical teams, cross-functional stakeholders, and leadership.

Benefits

Competitive benefits package designed to support health, well-being, work-life balance, and family needs.
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 a discretionary annual bonus program and may receive equity awards.
Estimated U.S. base salary range of $135,000–$155,000.