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Instrument Software Engineer Jobs (NOW HIRING)

Protingent

Embedded Software Engineer

Pasadena, CA · On-site

$120K - $150K/yr

Design and implement software that communicates with connected systems using SCPI (Standard Commands for Programmable Instruments) and VISA (Virtual Instrument Software Architecture) protocols

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Instrument Software Engineer information

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$12.5K

$104.9K

$164K

How much do instrument software engineer jobs pay per year?

As of Sep 13, 2026, the average yearly pay for instrument software engineer in the United States is $104,896.00, according to ZipRecruiter salary data. Most workers in this role earn between $77,500.00 and $131,500.00 per year, depending on experience, location, and employer.

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Cities with the most Instrument Software Engineer job openings:

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Infographic showing various Instrument Software Engineer job openings in the United States as of July 2026, with employment types broken down into 96% Full Time, 1% Part Time, and 3% Contract. Highlights an 87% Physical, 5% Hybrid, and 8% Remote job distribution, with an average salary of $104,896 per year, or $50.4 per hour.

Lead Instrument Software Engineer

Carlsbad, NM • On-site

Protillion Biosciences
Biotechnology Research and Development • 1 - 10 employees
Learn more about Protillion Biosciencesexternal

$155K - $205K/yr

Full-time

Re-posted 9 days ago

Job description

About Us:

Join our dynamic and innovative team at Protillion Biosciences, where we are pioneering a revolutionary high-throughput system for therapeutic development. We are dedicated to transforming the landscape of drug discovery with cutting-edge technology and a collaborative work environment.

About the Role:

We are seeking an experienced scientific instrument software engineer to lead software development of our advanced high-throughput protein analysis platform.

Job Responsibilities:

  • Lead instrument control software development for a scientific instrument platform.
  • Work closely with scientific and engineering peers, develop software development plans that include project objectives, scope, requirements, deliverables, schedule and milestones.
  • Be directly responsible to drive execution of all aspects of the software development lifecycle: requirements analysis, architecture, design, coding, documentation, testing, deployment, configuration management, and sustainment.

Requirements:

  • BS/BA Computer Science, Computer Engineering, Electrical/Mechanical/Chemical Engineering or Physics with 8+ years' experience, or MS/Ph.D. with 6+ years' experience.
  • Extensive demonstrable experience in developing sophisticated software for complex scientific instruments or automated machinery.
  • Extensive experience with:
    • Python
    • Qt
    • Git, GitHub
    • Windows
    • Asynchronous programming
    • Image processing; ImageJ
    • Serial port communication
    • Agile methodologies

What We Offer:

  • Competitive salary and benefits package.
  • Opportunity to work on groundbreaking technology and novel therapeutics.
  • Collaborative and inclusive work environment.
  • Professional development and growth opportunities.

Protillion is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees.

Compensation Range: $155,000/yr - $205,000/yr

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