Systems Integration Engineer II/III

Quantum-Si•San Diego, CA

6d•$90,000 - $130,000•Onsite

About The Position

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.

Requirements

Bachelor’s degree in engineering (e.g., Electrical, Mechanical, Systems, Biomedical, or related field).
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.

Nice To Haves

Master’s degree is a plus.
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

Responsibilities

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.

Benefits

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
Discretionary annual bonus program
Equity awards