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Protein Engineer Jobs in Indiana (NOW HIRING)

Field Engineer - Food Packaging - Elkhart, IN Field Service Technician Mechanic Automated Candy & Protein Bar Food Packaging Lines Maintenance Repair Installation Machinery Flow Wrappers Pouchers ...

Bachelor's required or equivalent in scientific disciplines, of Biochemistry, Protein Chemistry, Biophysical Chemistry, Bioanalytical Chemistry, Microbiology, Analytical Chemistry, or Engineering.

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Showing results 1-20

Protein Engineer information

See Indiana salary details

$22.5K

$86.3K

$156.6K

How much do protein engineer jobs pay per year?

As of May 30, 2026, the average yearly pay for protein engineer in Indiana is $86,262.00, according to ZipRecruiter salary data. Most workers in this role earn between $59,058.00 and $108,742.00 per year, depending on experience, location, and employer.

What does a Protein Engineer do?

A Protein Engineer designs and modifies proteins for specific functions in fields like medicine, biotechnology, and bioengineering. They use computational modeling, molecular biology techniques, and biochemical assays to improve protein stability, activity, or binding properties. Their work is crucial for developing new therapeutics, enzymes, and biomaterials for various industries.

What are the key skills and qualifications needed to thrive in the Protein Engineer position, and why are they important?

To thrive as a Protein Engineer, you need expertise in molecular biology, biochemistry, and protein structure-function analysis, often supported by an advanced degree in a relevant scientific field. Familiarity with tools such as protein modeling software, high-throughput screening systems, and genetic engineering techniques is commonly required. Attention to detail, strong analytical thinking, and effective teamwork are valuable soft skills in this role. These abilities are crucial for designing, optimizing, and testing proteins with desired properties, ensuring impactful contributions to research or product development.

What are the typical daily tasks and projects for a Protein Engineer?

Protein Engineers typically spend their days designing and conducting experiments to modify and improve protein characteristics, analyzing data from assays, and collaborating with cross-functional teams such as molecular biologists and biochemists. Their work often involves using specialized laboratory equipment, computational modeling tools, and maintaining detailed records of their experimental results. Projects may include developing enzymes for industrial processes, optimizing therapeutic proteins, or engineering innovative biomaterials. The pace can be dynamic, with a mix of independent bench work and group meetings to discuss progress, troubleshoot challenges, and plan next steps. This collaborative environment offers opportunities to learn from peers and contribute to cutting-edge scientific advancements.
What are the most commonly searched types of Protein Engineer jobs in Indiana? The most popular types of Protein Engineer jobs in Indiana are:
Infographic showing various Protein Engineer job openings in Indiana as of May 2026, with employment types broken down into 96% Full Time, and 4% Part Time. Highlights an 89% Physical, and 11% Remote job distribution, with an average salary of $86,262 per year, or $41.5 per hour.
Principal Process Engineer, Parenteral Drug Product Development

Principal Process Engineer, Parenteral Drug Product Development

Lilly

Indianapolis, IN

Full-time

Medical, Dental, Vision, Life, Retirement, PTO

Posted 24 days ago


Eli Lilly and Company rating

8.8

Company rating: 8.8 out of 10

Based on 62 frontline employees who took The Breakroom Quiz

11th of 70 rated pharmaceutical


Job description

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We're looking for people who are determined to make life better for people around the world.

Overview

At Lilly, we serve an extraordinary purpose.We make a difference for peoplearound the globeby discovering,developingand delivering medicines that helpthemlive longer, healthier, more active lives. Not only do we deliver breakthrough medications, but you also can count on us to develop creative solutions to support communities through philanthropy and volunteerism.

Position Summary

The main purpose and objectives of the Lilly Bioproduct Research and Development (BR&D) organization is focused on the development and commercialization of parenteral formulations of small molecules and large molecules such as monoclonal antibodies, novel therapeutic proteins and peptides. The organization is also committed to the development of genetic medicines which includes active investments in oligonucleotide development, nanomedicines for tissue specific targeting and other gene delivery strategies. The drug product team is also investing in building new platforms to support complex formulations such as lipid nanoparticles (LNPs), antibody drug conjugates, AAV, and other non-viral vector delivery vehicles.

We are seeking a highly motivated candidate for the position of Principal Process Engineer, Biologics Drug Product Development, located in Lilly Technology Center, Indianapolis.

Responsibilities

  • Develop parenteral drug product clinical manufacturing processes along with the associated control strategies.

  • Collaborate with cross-functional team members including but not limited to formulation development, clinical manufacturing, delivery devices, analytical development, RA and external CDMO, etc. to support clinical manufacturing and process validation to enable regulatory submission.

  • Design and execute manufacturing related process studies to determine process parameters and define processes to enable clinical manufacturing

  • Lead and/or assist tech transfer activities including but not limited to evaluating contact material compatibility, internal and CDMO capacity, authoring tech transfer documents, as well as reviewing batch records for drug products and placebos.

  • Author or coauthor and maintain process development technical documents.

  • Collaborate with cross functional team to help develop manufacturing process control strategies, process performance criteria, and capability criteria.

  • Collaborate with tech/mfg service team to support process qualification including defining process qualification and control strategy as well as providing onsite oversight of manufacturing.

  • Co-author or author drug product process development tech reports and regulatory submissions of IND, BLA or NDA as well as provide tech support in addressing any regulatory inquires.

  • Support and take part in evaluation and implementation of departmental initiatives to promote technical excellence.

  • Support evaluation and implementation of available new technologies applicable to drug product development portfolio from clinical to commercialization.

  • Understand and comply with corporate, divisional, and departmental procedures, including good manufacturing practices, safety, and other applicable regulations, and participate in the establishment and maintenance of departmental Quality systems.

  • Maintain an awareness of the proper use and maintenance of processing and laboratory equipment in the development facility. Properly address safety and environmental issues.

Basic Requirements

  • B.S. or M.S. in Pharmaceutical Chemistry or Engineering with related industry experience. B.S. with minimal 5 yrs and M.S. with minimal 3 yrs experience.

  • PhD will not be considered at this job level.

  • Working knowledge and understanding of parenteral product development is required.

  • Qualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1.

Additional Preferences

  • Good understanding of cGMP requirements, and ICH guidelines is highly preferred.

  • Good understanding of stability and potential degradation pathway of protein and peptides, etc. is a plus.

  • Working knowledge and experience in handling and developing ADC and mRNA LNP manufacturing process is highly preferred.

  • Sound understanding of statistics and data management is a plus.

  • Effective oral and written communication skills are essential.

Additional Information

Physical Demands/Travel:

The physical demands of this job are consistent with a lab environment.

The physical demands here are representative of those that must be met by an employee to successfully perform the essential functions of this job.

Work Environment:

This position's work environment is in a laboratory environment.

The work environment characteristics described here are representative of those an employee encounters while performing the essential functions of this job.

*To perform this job successfully, an individual must be able to perform the role and responsibilities satisfactorily. The requirements listed above are representative of the knowledge, skill, and/or ability required. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.


Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women's Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.

Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is

$79,500 - $148,500

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly's compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

#WeAreLilly


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About Eli Lilly

Sourced by ZipRecruiter

Eli Lilly, based in Indianapolis, IN, US, is one of the pioneers in the pharmaceutical industry with a rich history dating back to 1876. This global pharmaceutical company focuses on discovering, developing, manufacturing and selling pharmaceutical products in approximately 120 countries. The company's product categories include endocrinology, oncology, cardiovascular, neuroscience, and immunology. Having invested over $9 billion in research and development in the past decade, Eli Lilly is also committed to creating high-quality medicines that meet real needs. As a recipient of several awards and recognitions, Eli Lilly is known for its focus on life-saving research and drug development. Their mission is to make medicines that help people live longer, healthier, and more active lives.

Industry

Pharmaceutical product wholesalers

Company size

10,000+ Employees

Headquarters location

Indianapolis, IN, US

Year founded

1876