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

As part of our team, your core responsibilities will be:

Scientific Systems Integration and Characterization:

• 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.

Surface Chemistry and Material Interface Characterization:

• 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.

Reagent and Sample Stability

• 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.

Experimental Design and Statistical Analysis:

• 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 clearly communicate performance trends, variability, scientific risk, conclusions, and recommendations.

Cross-Functional Scientific Leadership:

• Lead cross-functional investigations with Surface Chemistry, Reagent Development, Applications, Consumables, Engineering, Software, Quality, Manufacturing, Operations, and Customer Success, translating system-level observations into focused studies, integration strategies, and evidence-based conclusions.

Test Method and Protocol Development:

• Develop reproducible experimental protocols, characterization plans, test methods, controls, acceptance criteria, analysis methods, and troubleshooting workflows that support rigorous investigations and defensible technical conclusions.

System Verification, Validation, and Reliability:

• Design and execute V&V, characterization, robustness, reliability, and regression studies demonstrating that integrated sample, reagent, consumable, surface, and workflow 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.

Customer-Relevant Workflow Evaluation:

• 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.

Technical Documentation and Communication

• 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 clearly to technical teams, cross-functional stakeholders, and leadership.

Qualifications:

• 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 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, with demonstrated experience integrating or troubleshooting assays, reagents, samples, materials, consumables, or automated life-science instrumentation.

• Demonstrated 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, with the ability to manage multiple workstreams independently and collaborate effectively across scientific and engineering teams.

• Strong technical communication skills and the ability to explain complex scientific findings to multidisciplinary audiences.

• Detail-oriented, objective, and rigorous approach to experimentation, data interpretation, and documentation.
• Travel requirement of up to 20 percent, including overnight and occasional international travel

Preferred qualifications:

• 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 the evaluation of 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.

Compensation and Benefits

The estimated base salary range for this position in the United States is $135,000 - $155,000. In addition to base salary, full-time employees are eligible to participate in Quantum-Si's discretionary annual bonus program and may receive equity awards as part of the total compensation package. Actual compensation will be determined based on a variety of factors, including, but not limited to, the position level, relevant skills, knowledge, experience, qualifications, geographic location, internal equity, and market data.

Quantum-Si also offers a competitive benefits package designed to support employees' health, well-being, work-life balance, and family needs. Benefits include:

• 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 & dismemberment (AD&D) insurance

• Short-term and long-term disability coverage

• Employee Assistance Program (EAP) resources to support personal and professional well-being

• Discretionary paid time off and company-paid holidays

• Parental leave to support employees welcoming and caring for a new child

• 401(k) retirement savings plan with both pre-tax and Roth contribution options

Additional Information 

Candidates must be authorized to work in the United States. Quantum-Si does not provide employment-based immigration sponsorship of any kind for this position, including support for applicants currently pursuing permanent residency (Green Card sponsorship). 

Quantum-Si does not accept unsolicited agency resumes. 

Quantum-Si is an E-Verify and equal opportunity employer regardless of race, color, ancestry, religion, gender, national origin, sexual orientation, age, citizenship, marital status, disability or Veteran status. All your information will be kept confidential according to EEO guidelines.