---
title: 'Systems Integration Engineer II/III at Quantum-Si'
canonical: 'https://feeny.ai/job/systems-integration-engineer-ii-iii-quantum-si-san-diego-0w0205kv6jzm'
type: 'job'
last_seen: '2026-09-09'
---

# Systems Integration Engineer II/III at Quantum-Si

- **Company:** Quantum-Si
- **Location:** San Diego, CA
- **Posted:** 2026-09-02
- **Last confirmed live:** 2026-09-09
- **Apply:** https://job-boards.greenhouse.io/quantumsi25/jobs/6179774004

## 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.
- 2–5yearsof 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

## Compensation and Benefits

The estimated base salary range for this position in the United States is $90,000- $130,000. In addition to base salary, full-time employees are eligible to participate in Quantum-Si's discretionary annual bonus program and may receive equity awards as part of the total compensation package. Actual compensation will be determined based on a variety of factors, including, but not limited to, the position level, relevant skills, knowledge, experience, qualifications, geographic location, internal equity, and market data.

Quantum-Si also offers a competitive benefits package designed to support employees' health, well-being, work-life balance, and family needs. Benefits include:

- 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

Additional Information

Candidates must be authorized to work in the United States. Quantum-Si does not provide employment-based immigration sponsorship of any kind for this position, including support for applicants currently pursuing permanent residency (Green Card sponsorship).

Quantum-Si does not accept unsolicited agency resumes.

Quantum-Si is an E-Verify and equal opportunity employer regardless of race, color, ancestry, religion, gender, national origin, sexual orientation, age, citizenship, marital status, disability or Veteran status. All your information will be kept confidential according to EEO guidelines.

## About Quantum-Si

## Company Overview
- **One-liner**: Quantum-Si is pioneering the post-genomic era by making single-molecule protein sequencing accessible through its benchtop Platinum and Platinum Pro instruments.
- **Entity Type**: Public (NASDAQ: QSI)
- **Headquarters**: Branford, Connecticut, United States
- **Founded**: 2013
- **Founders**: Jonathan Rothberg

## Core Business
- **Primary industry**: Biotechnology Research / Life Sciences Tools (Proteomics)
- **Target customers**: B2B; academic research labs, pharmaceutical and biotechnology companies, core facilities, and drug development organizations.
- **Mission or purpose statement**: To power the post-genomic era of biology by making next-generation protein sequencing (NGPS) accessible to every lab, everywhere, enabling breakthroughs in drug discovery, diagnostics, and human health.

## Products & Services
- **Platinum® Pro**: An advanced benchtop next-gen protein sequencer (NGPS) delivering single-molecule resolution with real-time kinetic insights. It features a simplified workflow (less than three hours of hands-on time), a user-friendly touchscreen interface, and flexible data analysis (local or cloud-based). Designed for variant detection, protein identification, and post-translational modification (PTM) analysis.
- **Platinum®**: The world’s first next-gen protein sequencing instrument, enabling single-molecule, single-amino-acid resolution for proteomics research.
- **Proteus™ Platform**: A next-generation platform (announced in partnership with Cell Signaling Technology) focused on advancing post-translational modification (PTM) analysis.
- **Protein Barcoding**: A solution for simultaneously characterizing multiple protein variants, increasing throughput for screening and therapeutic development, including applications in drug delivery (LNPs, AAV capsids) and antibody characterization.

## Market Standing
- **Valuation/Market Cap**: $109.7 million (as of mid-2026) [linkedin.com]
- **Key Metric**: Annual Revenue of $2.4 million (public company) [linkedin.com]
- **Total Funding**: $1.065 billion (including post-IPO equity rounds) [linkedin.com]
- **Notable Investors/Partners**: HighCape Capital Acquisition Corp (parent), Cell Signaling Technology (strategic partner for PTM analysis), 4Catalyzer (affiliated incubator).
- **Growth Signals**: 
    - Publicly traded on NASDAQ (QSI) since June 2021.
    - Announced a strategic partnership with Cell Signaling Technology in June 2026 to advance PTM analysis on the Proteus platform [quantum-si.com].
    - Expanding commercial presence with a roadshow for the Proteus platform [quantum-si.com].
    - Named "2023 Proteomics Company of the Year" and "Innovation by Design 2023" [quantum-si.com].
    - Active hiring for senior commercial and field roles, indicating a push to scale go-to-market.

## Competitive Advantages
- **First-mover in NGPS**: Quantum-Si is the first company to bring a next-generation protein sequencing (NGPS) platform to market, offering single-molecule resolution that traditional mass spectrometry and Edman degradation cannot achieve.
- **Simplified Workflow**: The platform requires less than three hours of hands-on time and no dedicated lab space or specialized expertise, making advanced proteomics accessible to a broader range of labs.
- **Unique Kinetic Profiling**: Uses real-time, single-molecule kinetic signatures to detect protein variants, post-translational modifications, and proteoforms, providing deeper functional insights than antibody-based or mass-spec methods.
- **Integrated AI**: Blends biology, chemistry, and artificial intelligence to drive data analysis and interpretation.

## Strategic Focus
- **Commercial Expansion**: Scaling the commercial team (hiring field application scientists, service engineers, and business development managers) to drive adoption of the Platinum and Proteus platforms globally.
- **Partnership Development**: Deepening collaborations with key players like Cell Signaling Technology to expand applications in PTM analysis and drug development.
- **Platform Evolution**: Advancing the Proteus platform and expanding the protein barcoding solution for high-throughput screening in therapeutic development (e.g., LNPs, AAV capsids).
- **Market Penetration**: Moving beyond early adopters to broader academic and pharmaceutical markets, with a focus on making proteomics accessible without dedicated lab space or specialized expertise.

## Why Work Here
- **Culture**: Described as dynamic, collaborative, and purpose-driven, with a focus on innovation and solving complex scientific challenges. Values include "Never Settle," "Embrace Change," "Succeed Together," "Stand Up," and "Speak Up" [quantum-si.com].
- **Mission-Driven**: Employees are motivated by the potential to transform human health and make a global impact through accessible protein sequencing.
- **Benefits & Perks**: 100% fully covered medical/dental/vision, generous HSA contribution on HDHP, 401K plan, generous parental leave, flexible paid time off, short/long-term disability, and company-sponsored life insurance [quantum-si.com].
- **Equity**: 100% of employees are stakeholders, aligning team members with company success.
- **Work Environment**: Dynamic and collaborative culture. Roles are a mix of on-site (San Diego, CA; Branford, CT) and remote (e.g., Field Application Scientist, Northwest AMR). The company emphasizes transparency, adaptability, and a purpose-driven mission.
- **Headcount**: 153 employees, with a +1.6% YoY growth. The team is primarily US-based (75%) with a presence in France, UK, Germany, Spain, Belgium, and Singapore [linkedin.com].

## Sources
1. [quantum-si.com](https://www.quantum-si.com/)
2. [quantum-si.com/about](https://www.quantum-si.com/about/)
3. [quantum-si.com/careers](https://www.quantum-si.com/about/careers/)
4. [linkedin.com/company/quantum-si](https://www.linkedin.com/company/quantum-si)
5. [job-boards.greenhouse.io/quantumsi25](https://job-boards.greenhouse.io/quantumsi25)

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