Principal Chemist – GMP Analytical Method Development and Testing Lilly Medicine Foundry

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us. 

Organization and Position Overview

Lilly recently announced a $4.5 billion investment to create the Lilly Medicine Foundry, a new center for advanced manufacturing and drug development. The first-ever facility of its kind, combining research and manufacturing in a single location, the Medicine Foundry will allow Lilly to further develop innovative solutions to optimize manufacturing processes and increase capacity for clinical trial medicines, while also reducing costs and environmental impact.

The analytical team supporting Cleaning Validation delivers the scientific evidence and timely results that allow Foundry equipment to be released safely and on schedule. In this role, we are seeking an experienced, innovative, and motivated chemist to rapidly develop, validate, and routinely run HPLC/UPLC methods (UV, CAD, ELSD, and other detection, with mass spectrometry for trace-level and low-chromophore residues) in a GMP environment, supporting cleaning verification and validation across multiple modalities: small molecules, biomolecules, peptides, oligonucleotides, and high potency compounds.

This is a hands-on, onsite laboratory role that combines method development with routine GMP testing at the tempo of manufacturing. It offers significant technical ownership and the opportunity to build analytical capabilities from the ground up at a first-of-its-kind facility supporting clinical Phase 1 through Phase 3 supply. You will collaborate with Manufacturing, Quality, and Process Development, and your technical leadership will influence how cleaning validation is executed as the Foundry moves from startup to steady-state operations.

 

Responsibilities

Top candidates for this position will be expected to:

• Perform hands-on laboratory work in a GMP environment to design, develop, and implement analytical methods and testing that support the cleaning validation strategy across multiple modalities, including small molecules, biomolecules, peptides, oligonucleotides, and high potency compounds.
• Rapidly develop and qualify HPLC/UPLC methods with UV, CAD, ELSD, and other detection techniques for cleaning validation and verification of API, intermediate, and cleaning agent residues.
• Apply mass spectrometry (LC-MS) to develop sensitive, selective methods for trace-level residues, degradants, and compounds lacking a UV chromophore, and to support investigations.
• Perform routine GMP testing of swab and rinse samples to support timely equipment release at the tempo of manufacturing, including sample receipt, analysis, data review, and reporting.
• Develop and execute swab and rinse recovery studies and sample preparation approaches suited to each modality, and establish method sensitivity (LOD/LOQ), linearity, accuracy, precision, specificity, and solution stability appropriate for residue limits.
• Safely handle and analyze high potency compounds using appropriate containment and HSE practices, and develop methods sensitive enough to meet low residue limits.
• Write and execute method qualification/validation protocols and reports, author analytical procedures, and support quality investigations, audits, and inspections in compliance with cGMP and data integrity (ALCOA+) expectations.
• Collaborate with cleaning validation, Manufacturing, Quality, and Process Development partners to define analytical requirements, understand acceptance limits, and prioritize testing against the manufacturing schedule.
• Lead technology transfer of methods to the Foundry quality control laboratory, other Lilly sites, and external partners, and provide technical oversight of external analytical work to ensure methods are scientifically sound and fit for purpose.
• Troubleshoot chromatographic and mass spectrometric methods and instrumentation, and lead investigation of out-of-trend or out-of-specification results.
• Introduce platform methods and streamlined workflows that accelerate method development, validation, and routine testing, and improve robustness across products.
• Mentor and train junior team members and analysts, fostering technical growth and knowledge sharing.
• Plan and manage development and testing priorities, coordinate instrument and laboratory capacity, contribute to Foundry laboratory readiness, and communicate progress.
• Flex work hours as needed to meet operational demands, including support during shutdowns, weekends, and overnight operations.

 

Basic Requirements:

• M.S. in Analytical Chemistry, Chemistry, Organic Chemistry, Biochemistry, Pharmaceutical Sciences, or a closely related STEM field with 5+ years of relevant experience in the pharmaceutical industry; or
• B.S. in Analytical Chemistry, Chemistry, Organic Chemistry, Biochemistry, Pharmaceutical Sciences, or a closely related STEM field with 8+ years of relevant experience in the pharmaceutical industry.
• Hands-on experience developing HPLC and/or UPLC methods with UV and other detectors such as CAD or ELSD.
• Hands-on experience with liquid chromatography-mass spectrometry (LC-MS) for method development or sample analysis.
• Experience performing routine analytical testing and method development/qualification/validation in a GMP laboratory.
• Working knowledge of cGMP, data integrity principles, and good documentation practices.
• 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:

• Direct experience with cleaning validation or cleaning verification analytical methods, including swab/rinse recovery studies and trace-level residue analysis.
• Experience analyzing multiple modalities, including small molecules, biomolecules, peptides, oligonucleotides, and high potency compounds.
• Experience working with high potency compounds, including containment practices and low residue limit methods; an understanding of residue limit concepts (e.g., health-based exposure limits and MACO).
• Deep fundamental understanding of and hands-on experience with reversed-phase, HILIC, ion-pairing, ion exchange, and/or size-exclusion chromatography, and universal detection techniques such as CAD or ELSD.
• Working knowledge of complementary techniques such as TOC, conductivity, UV/Vis, or FTIR.
• Proficiency with chromatography data systems (e.g., Empower) and electronic laboratory notebooks.
• Demonstrated ability to develop methods quickly using structured, risk-based, or Quality by Design approaches, and to reduce cycle times in analytical workflows.
• Experience with method transfer, instrument qualification, or laboratory start-up.
• Strong hands-on technical skills, learning agility, and the ability to prioritize laboratory workload and manage ambiguity.
• Strong communication skills and the ability to provide cross-functional leadership, while working both independently and collaboratively in a dynamic laboratory environment.
• Passion for applying analytical chemistry through hands-on laboratory work to solve real-world pharmaceutical manufacturing challenges and improve patient outcomes.

 

Other Information:

• Initial location in Carmel, IN
• Permanent location at the new Lilly Medicines Foundry in Lebanon, Indiana. 
• Position is onsite only and laboratory-based; remote or hybrid work is not available.
• Requires flexibility to adjust work hours to meet operational demands, including support during shutdowns, weekends, and overnight operations as needed.
• Potential exposure to chemicals, allergens, high potency compounds, and loud noises.

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 (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).

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

$66,000 - $171,600

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.

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