Systems Integration Engineer II/III Hands-On Cross-Functional

Quantum-Si; San Diego (CA); On-site; USD 90,000 - 130,000; Full time

Benefits offered by this job

Comprehensive medical, dental, and vis

Health Savings Account and Flexible

Company-paid life and AD&D insurance

Disability coverage

EAP resources

Paid time off and holidays

Parental leave

401(k) retirement plan

Job summary

Quantum-Si in San Diego, California seeks a Systems Integration Engineer to drive end-to-end integration for Proteus, combining hardware, software, firmware, optics, and chemistry in customer workflows.

You will perform testing, troubleshooting, and data analysis, collaborating with cross-functional teams to improve validation protocols and ensure reliability of the next-generation sequencing platform.

Qualifications

• 2-5 years of experience in system integration, testing, or related engineering roles.
• Bachelor’s degree in engineering; Master’s degree is a plus.
• 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; detail-oriented; proactive problem solving and continuous improvement.

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.

Skills

System integration

Testing

Troubleshooting

Python scripting

Data analysis

Education

Bachelor’s degree in engineering

Master’s degree is a plus

Tools

Jira/Confluence

Job description

Quantum-Si in San Diego, California seeks a Systems Integration Engineer to drive end-to-end integration for Proteus, combining hardware, software, firmware, optics, and chemistry in customer workflows.

You will perform testing, troubleshooting, and data analysis, collaborating with cross-functional teams to improve validation protocols and ensure reliability of the next-generation sequencing platform.