> Markdown version of [/jobs/ext/2691496-systems-integration-engineer](https://www.wearedevelopers.com/jobs/ext/2691496-systems-integration-engineer). Every page supports `.md` or `Accept: text/markdown`. Links point to the HTML versions so they work for humans too. Agent guide: [/agents.md](https://www.wearedevelopers.com/agents.md). --- # Systems Integration Engineer - **Company:** Quantum-si, Inc. - **Location:** San Diego, CA, United States - **Experience:** Experienced - **Salary:** $90,000.0 - $130,000.0 - **Contract:** Permanent contract - **Skills:** Data Analysis, Confluence, JIRA, Software Documentation, Software Debugging, Firmware, Failure Mode Effects Analysis, Imaging Technology, Issue Tracking Systems, Log Analysis, Minitab, Software Reliability Testing, E2e Testing, Requirements Management, Verification and Validation (Software), System Testing, Systems Integration, Visual Systems, Scripting, JMP (Statistical Software), System-level Testing, Integration Frameworks - **Published:** September 3, 2026 - **Apply:** https://job-boards.greenhouse.io/quantumsi25/jobs/6179774004 ## About the Role * 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. Preferred qualifications: * 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 Physical Demands/Work Conditions * 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 ## 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. ## Related Videos - [Improving quality with Agentic AI with Rovo Dev and Xray](https://www.wearedevelopers.com/videos/2005-improving-quality-with-agentic-ai-with-rovo-dev-and-xray) - [Playing Pong on a shoulder press machine](https://www.wearedevelopers.com/videos/100140-playing-pong-on-a-shoulder-press-machine) - [Quantum DevOps - Quantum Application Development](https://www.wearedevelopers.com/videos/1441-quantum-devops-quantum-application-development) - [Collaboration Quantified: Lessons from Open Source Developer Networks](https://www.wearedevelopers.com/videos/1422-collaboration-quantified-lessons-from-open-source-developer-networks) - [Quantum Computing - The tiny and the big challenges](https://www.wearedevelopers.com/videos/934-quantum-computing-the-tiny-and-the-big-challenges) - [Agent Smith Gets Hardware: Autonomous IoT Hacking From Debug Port to Cloud API](https://www.wearedevelopers.com/videos/100258-agent-smith-gets-hardware-autonomous-iot-hacking-from-debug-port-to-cloud-api) ## Related Articles - [How We Built a Worry-Free System That Runs for 10+ Years – And What We’d Do Again](https://www.wearedevelopers.com/magazine/751-how-we-built-a-worry-free-system-that-runs-for-10-years-and-what-we-d-do-again) - [The 12 Best Jobs for Software Engineers](https://www.wearedevelopers.com/magazine/401-the-12-best-jobs-for-software-engineers) - [Now is the time for industrialized software development](https://www.wearedevelopers.com/magazine/601-now-is-the-time-for-industrialized-software-development) - [What is Software Engineering?](https://www.wearedevelopers.com/magazine/289-what-is-software-engineering) - [Is Software Engineering Over-Saturated?](https://www.wearedevelopers.com/magazine/418-is-software-engineering-over-saturated) - [The Fastest-Growing Tech Sectors to Look Out for in 2025](https://www.wearedevelopers.com/magazine/373-the-fastest-growing-tech-sectors-to-look-out-for-in-2025)