---
title: 'Senior Director of Engineering at Quantum-Si'
canonical: 'https://feeny.ai/job/senior-director-of-engineering-quantum-si-san-diego-1g62mxw2mfzt'
type: 'job'
last_seen: '2026-09-09'
---

# Senior Director of Engineering at Quantum-Si

- **Company:** Quantum-Si
- **Location:** San Diego, CA
- **Posted:** 2026-08-20
- **Last confirmed live:** 2026-09-09
- **Apply:** https://job-boards.greenhouse.io/quantumsi25/jobs/6148482004

## Job description

Quantum-Si is seeking an experienced Senior Director of Engineering to drive innovation in next generation protein sequencing instrumentation and consumables. This leader will grow and develop the engineering team to build well-designed instrumentation with high quality and reliability. The Senior Director of Engineering will oversee all aspects of mechanical, electrical, optical, and fluidics engineering, as well as consumable engineering, systems integration,. This role requires a strategic leader with a deep understanding of complex engineering disciplines and a proven track record of bringing innovative scientific instruments to market. The ideal candidate will possess exceptional leadership skills, technical expertise, and a passion for driving technological advancements in scientific instrumentation and consumables used to measure single molecules in biochemical assays.

As part of our team, your core responsibilities will be:

- Lead, mentor, and develop high performing teams of engineers, systems integration scientists, and instrument software developers, fostering a culture of collaboration, creativity, quality, and continuous improvement
- Develop and execute a comprehensive engineering strategy that aligns with the company’s vision and business goals
- Collaborate with other departments, including R&D, Commercial, and Operations, as well as 3rd party vendors to align engineering efforts with market needs and business goals
- Oversee the planning, execution, and successful completion of engineering projects that are delivered on time, within scope, and within budget
- Provide technical guidance and expertise in the development of scientific instruments, ensuring products meet rigorous quality and regulatory standards
- Oversee the development of instrument control software and its integration with hardware and consumables
- Lead the systems integration team to verify new instrumentation, consumables, and software, as well as maintain the existing fleet of instruments

## Qualifications

- Bachelor’s or master’s degree in engineering or a related field.
- Minimum of 8 years of experience in engineering leadership roles and 12 years of engineering experience, preferably within the biotechnology or scientific instrumentation industries.
- Proven track record of managing complex engineering projects from concept to commercialization and transfer to manufacturing
- Strong understanding of product development processes, quality assurance, and regulatory requirements.
- Ability to work in a fast paced, dynamic environment and manage multiple priorities.
- Exceptional communication skills, both written and verbal, with the ability to effectively communicate complex concepts to diverse audiences.
- Excellent leadership and team management skills with a history of building and developing high performing teams.
- Ability to travel up to 25% of the time.

The estimated base salary range for this position in the United States is $275,000- $300,000. 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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