Senior Scientist Protein Science & Engineering Large Molecule Biologics

Company: Eli Lilly and Company
Location: San Francisco
Posted on: March 28, 2026

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. Job Description Job Title: Advisor, Bioanalytical Research Organization Overview: The Bioanalytical Research Group (BAR) at Lilly’s research facility in South San Francisco, CA is seeking a strong scientist skilled in protein mass spectrometry to deliver innovative ways in our evaluation of the ADME properties of therapeutic proteins and antibody-drug-conjugates (ADCs). The team works with Investigative ADME, Toxicology, Oncology, and Biotechnology Discovery Research to discover and characterize optimal ADC candidates to advance to clinical testing. Primary Responsibilities: The development and application of QQQ and high-resolution LC/MS approaches to characterize the PK, biotransformation, and biodistribution of ADC drug candidates in pre-clinical animal models. The application of mass spectrometry and wet biochemistry to answer questions related to target engagement and mechanism of action of ADCs. Support Bio-Analysis sample preparation, experimental design, and mass-spec analysis of biological samples as well as data analysis/interpretation from in-vivo studies from triple-quad mass spectrometers (Sciex 7500). Maintain a high level of productivity in a laboratory setting. This role is 100% on site in South San Francisco and is lab based, but will have opportunities to present the data to project teams. Counsel the research activities of and mentoring junior laboratory staff in mass spectrometry, bioanalysis, and protein chemistry. Serving as the Bioanalytical Project Lead for discovery projects requiring input from a highly qualified scientist on issues related to PK/PD, biotransformation, and biodistribution. Characterization of recombinant proteins, antibodies, and ADCs using intact-MS and peptide mapping for routine QC using high-res mass spec platforms (Oribtrap). Job Requirements: Ph.D. in biochemistry/molecular biology, bioengineering, biology, pharmacology, chemistry, or scientific field. Experience using mass spectrometry-based methods to support the bio-analysis of ADCs and therapeutic proteins. This should include developing and running MRM as well as intact, high-resolution MS LCMS of ADCs from biological matrices to evaluate the biotransformation of ADCs in animal models. Experience supporting multiple ADC drugs drug development programs, including assessing PK, Efficacy, and tox profiles in preclinical models and communicating data to project teams. Experience with analyzing and reporting analytical data, presenting data to colleagues and collaborators, and serving as a subject area expert in mass spec and analytical approaches. Experience developing methods, operating, and the routine maintenance/troubleshooting of Thermo Orbitrap and Sciex QQQ mass spectrometers is required. Experience with a wide variety of sample preparation techniques including SPE, and immunoaffinity/hybridization capture techniques. Experience with automation (TECAN, KingFisher, Hamilton) highly preferred Experience with high throughput plate-based assays working on both large and small molecules. Additional Experience is Preferred: Knowledge of MS-informatic approaches to interpret complex data sets (Proteome Discoverer, Protein Metrics, DAR calculations, Mass MetaSite, Biopharma Finder, e.g.) Strong organizational and planning regarding analysis, record keeping, multi-tasking workflows, and data analysis skills is needed. Understanding of ADC competitive landscape. Knowledge of the ADME principles of biotherapeutic drugs. Prior experience with MS based imaging techniques Experience with proteomics methods, DDA, nano-LC, DIA, or similar workflows in a drug discovery setting Cell Culture experience is a plus Experience with R, python, or other biostatistical packages for data visualization is a plus. 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 $151,500 - $222,200 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

Keywords: Eli Lilly and Company, San Francisco , Senior Scientist Protein Science & Engineering Large Molecule Biologics, Science, Research & Development , San Francisco, California