Systems Integration Engineer II​/III

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:

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…