Systems Integration Engineer II/III

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:   

• 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.

• 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.

• Assist in creating, refining, and executing test plans, protocols, acceptance criteria, and procedures that improve system validation, workflow robustness, and product reliability. 

• 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. 

• 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. 

• Evaluate instrument performance in workflows that reflect real customer use cases, including sample preparation interfaces, sequencing runs, data handoff, usability, reliability, and serviceability considerations. 

• Improve integration workflows, troubleshooting guides, test documentation, and knowledge-sharing practices to increase team efficiency, reproducibility, and readiness for product commercialization and field support. 

• Support system verification, validation, characterization, and reliability testing in accordance with documented procedures and product development requirements. 

• 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.

• 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 

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.