Systems Integration Engineer II/III

quantumsi25; San Diego (CA); On-site; USD 90,000 - 130,000; Full time

Job summary

Quantum-Si is seeking a Systems Integration Engineer to drive end-to-end integration testing for the Proteus platform. You will troubleshoot complex issues across hardware, software, firmware, optics and fluidics, and work with multidisciplinary teams to ensure reliable customer workflows.

Responsibilities include test plan development, data analysis, and documenting findings to support product readiness and field support.

Qualifications

• Bachelor's degree in electrical, mechanical, systems, biomedical or related field.
• 2–5 years of system integration, testing, or related engineering experience.
• Self-starter who can work independently and in teams.
• Experience integrating instrumentation with hardware, software, firmware, optics, and fluids.
• Proficiency in system-level testing, data analysis and structured test protocols.
• Familiarity with DOE, JMP/Minitab/Python for data analysis and statistics.

Responsibilities

• Execute and support end-to-end integration testing for Proteus hardware/software stack.
• Identify, analyze, and resolve moderately complex integration issues.
• Develop and refine test plans, criteria, and procedures.
• Collaborate with engineering, software, applications, and operations teams.
• Collect and interpret instrument performance data and run results.
• Evaluate workflows reflecting real customer use cases and improve robustness.

Skills

System integration

Troubleshooting

Data analysis

Cross-functional collaboration

Lab work

Python scripting

Communication

Education

Bachelor's degree in engineering

Master's degree preferred

Tools

Python

DOE

JMP

Minitab

Jira/Confluence

Job description

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 ca n 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.

Pre ferred qualifications:

Next Generation Sequencing, proteomics, single-molecule detection, or other complex life science instrument workflows and reagents; and/or o ptical 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, o