Systems Integration Engineer II/III

About the role

Quantum-Si is seeking a skilled and motivated Systems Integration Engineer to conduct, analyze, and improve system integration activities for Proteus, Quantum-Si’s next generation single molecule protein sequencing platform. This role requires hands-on execution, rigorous troubleshooting, and close collaboration across hardware, software, firmware, optics, chemistry, reagents, consumables, and applications teams to ensure the integrated system performs reliably in customer-relevant workflows.

Responsibilities

• System Integration Testing: Execute and support end-to-end integration testing for Proteus, ensuring hardware, software, firmware, optics, fluidics, consumables, reagents, and workflow components function cohesively and meet system performance requirements.
• Troubleshooting and Root-Cause Analysis: Identify, analyze, and resolve moderately complex system integration issues using structured root-cause methods, experimental evidence, instrument logs, run data, and collaboration with subsystem owners.
• Test Plan and Protocol Development: Assist in creating, refining, and executing test plans, protocols, acceptance criteria, and procedures that improve system validation, workflow robustness, and product reliability.
• Cross-Functional Collaboration: Work closely with engineering, R&D, software, applications, customer success, development partners and operations teams to resolve subsystem interdependencies and translate integration findings into actionable improvements.
• Data Analysis and Technical Reporting: Collect, analyze, and interpret instrument performance data, sequencing run outputs, failure modes, and integration metrics; prepare clear technical summaries that communicate findings, risks, and recommendations to stakeholders.
• Customer-Relevant Workflow Evaluation: Evaluate instrument performance in workflows that reflect real customer use cases, including sample preparation interfaces, sequencing runs, data handoff, usability, reliability, and serviceability considerations.
• Continuous Improvement and Documentation: Improve integration workflows, troubleshooting guides, test documentation, and knowledge-sharing practices to increase team efficiency, reproducibility, and readiness for product commercialization and field support.
• Instrument Verification and Validation: Support system verification, validation, characterization, and reliability testing in accordance with documented procedures and product development requirements.

Qualifications

• Bachelor’s degree in engineering (e.g., Electrical, Mechanical, Systems, Biomedical, or related field). Master’s degree is a plus.
• 2–5 years of experience in system integration, testing, or related engineering roles.
• Self-starter who can work independently, but who also functions well in a collaborative team environment.
• Experience integrating and debugging complex instrumentation involving hardware, software, firmware, optics, lasers, fluidics, motion control, consumables, and reagents.
• Proficiency in system-level testing, verification, validation, data analysis, and execution of structured test protocols.
• Experience with DOE, JMP/Minitab/Python-based analysis, FMEA, risk assessment, and statistical interpretation of system performance.
• Familiarity with Python scripting for data analysis, automation of test workflows, instrument log parsing, and visualization of system performance trends.
• Strong analytical and experimental troubleshooting skills, including the ability to interpret run data, logs, failure signatures, and subsystem interactions to drive root-cause resolution.
• Comfort working hands-on in the lab with integrated instruments, experimental workflows, prototype systems, and cross-disciplinary technical teams.
• Ability to document observations, deviations, test results, and recommendations clearly enough to support design decisions, issue tracking, and knowledge transfer.
• Strong communication and teamwork skills for effective collaboration across multidisciplinary teams.
• Detail-oriented approach with the ability to manage multiple tasks and priorities.
• Proactive problem-solving mindset with a focus on continuous improvement.

Preferred qualifications

• Next Generation Sequencing, proteomics, single-molecule detection, or other complex life science instrument workflows and reagents; and/or optical systems, imaging systems, fluorescence detection, or laser-based instrumentation.
• Semiconductor devices, sensor arrays, microfluidics, consumables, or chip-based platforms.
• Instrument control software, data analysis pipelines, requirements management, Jira/Confluence documentation, or formal issue triage processes.
• Experience working under quality-system expectations, including good documentation practices, issue tracking, deviation documentation, and controlled test protocols.
• Experience supporting product commercialization, reliability growth, field issue investigation, or customer-facing technical escalations.
• Experience working in fast-paced start-up or product development environments.

Physical Demands / Work Conditions

• Position is based in San Diego, California.
• Travel requirement of up to 20 percent, including overnight and occasional international travel.
• Ability to lift up to 50 pounds and work in laboratory environments.
• Exposure to biological samples and hazardous materials may be required.

Compensation and Benefits

• The estimated base salary range for this position in the United States is $90,000–$130,000. 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.