Mass Spectrometry Manager Jobs in Indiana (NOW HIRING)

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At Lilly, we serve an extraordinary purpose. We make a difference for people around the world by discovering, developing, and delivering medicines that help them live longer, healthier, more active lives. Within Cardiometabolic Research (CMR), our biomarker and translation laboratories generate high-quality molecular data across preclinical and clinical samples to characterize disease biology, support target and biomarker discovery, and inform the safety, efficacy, and pharmacology of therapeutic candidates from discovery through clinical development.
We are expanding our internal analytical capabilities and are seeking a highly motivated Postdoctoral Scientist to help establish and apply mass spectrometry (MS)-based proteomics within the group.
Purpose of the Job
This is a hands-on, fixed-term postdoctoral position focused on developing, implementing, and applying LC-MS-based proteomics and phosphoproteomics workflows to support biomarker research and the mechanistic characterization of metabolic disease biology. The successful candidate will take ownership of a high-resolution mass spectrometry platform, establish robust and reproducible quantitative proteomics capabilities within CMR, and work at the interface of analytical method development, preclinical biology, and translational biomarker science.
The role offers hands-on ownership of new analytical capabilities, close collaboration across cross-functional and cross-site scientific teams, and the opportunity to publish in peer-reviewed journals, with an expectation of one to two publications over the term. It provides high-impact scientific exposure and skill development at the intersection of quantitative proteomics, phosphoproteomics, and translational biomarker science.
Key Responsibilities

• Method Development & Platform Establishment - Develop, optimize, and validate LC-MS-based proteomics and phosphoproteomics workflows on high-resolution mass spectrometry instrumentation, including sample preparation, peptide and phosphopeptide enrichment (e.g., TiO₂, IMAC), and data-independent acquisition (DIA) methods optimized for preclinical sample types. Establish robust, reproducible, well-documented analytical pipelines and bring new capabilities online within the group.
• Quantitative Proteomics & Phosphoproteomics Execution - Implement global (bottom-up) proteomics and phosphoproteomics on preclinical samples with high data quality, reproducibility, and appropriate quality control. Maintain instrument readiness and performance through routine care, calibration, and troubleshooting.
• Data Analysis, Interpretation & Visualization - Process, analyze, and interpret large, multi-dimensional proteomic and phosphoproteomic datasets. Apply appropriate statistical methods, generate clear and insightful data visualizations to identify pathway-level and mechanistic signals, and translate results into actionable conclusions for project teams and decision-making forums.
• Scientific Documentation & Data Integrity - Maintain meticulous experimental records and thorough, prompt electronic lab notebook entries. Ensure clear traceability, data integrity, and compliance with group protocols, and document methods, QA/QC records, and standard operating procedures.
• Collaboration & Communication - Work as a proactive, team-oriented scientist within a highly collaborative research environment. Partner with colleagues operating complementary analytical platforms, coordinate on shared samples and workflows, and communicate findings through presentations, written summaries, and peer-reviewed publications, with opportunities for scientific exchange across sites and fields.
• Continuous Improvement & Innovation - Champion standardization, automation, and process improvement to enhance throughput, reproducibility, and data quality. Evaluate and adopt new methodologies and tools - including artificial intelligence (AI) tools - to strengthen laboratory workflows and data analysis.

Basic Requirements

• PhD in Biochemistry, Analytical Chemistry, Molecular Biology, or a closely related life sciences field (recently completed or nearing completion).
• Demonstrated hands-on expertise in LC-MS/MS-based proteomics and/or phosphoproteomics assay development and implementation.
• 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 Skills / Preferences

• Hands-on experience with high-resolution mass spectrometry platforms and data-independent acquisition (DIA) methods.
• Experience developing or applying phosphopeptide enrichment methods (e.g., TiO₂, IMAC).
• Familiarity with proximity-labeling proteomics (e.g., TurboID, BioID), or strong interest and skills for developing such methodology.
• Experience with proteomics data-analysis and informatics tools (e.g., Spectronaut, DIA-NN, MaxQuant, Perseus) and with statistical and visualization software (e.g., GraphPad Prism, JMP, R/Python).
• Experience preparing preclinical and tissue samples for MS-based analysis.
• Familiarity with complementary non-MS proteomics or biomarker platforms (e.g., Olink, immunoassays) and an understanding of orthogonal validation across technologies.
• Interest in metabolic and cardiometabolic disease biology.
• Familiarity with laboratory automation and liquid-handling systems.

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Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is
$58,000 - $123,200
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.
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