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Systems Integration Engineer II/III

San Diego, CA

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. 

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

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. 
  • 2–5yearsof experience in system integration, testing, or related engineering roles. 
  • Self-starterwho 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 communicationand 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, is preferred. 
  • 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  

  • This 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  

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.   

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