Principal Scientist, Mass Spectrometry

Moderna • Cambridge, MA

2d • $142,500 - $256,500 • Onsite

About The Position

Moderna is seeking a highly motivated Principal Scientist, Mass Spectrometry to join the Cancer Vaccine and Bioinformatics Research (CVBR) team and support preclinical research. This role combines significant hands-on laboratory work with scientific and technical leadership, cross-functional collaboration, and people management responsibilities. The successful candidate will develop and apply peptide-based liquid chromatography-mass spectrometry (LC-MS) proteomics approaches to address complex biological questions, advance research programs, support cross-functional mass spectrometry priorities within the team, and build and strengthen robust, scalable analytical capabilities that can be applied across Moderna’s portfolio. A key focus of the role will be evolving how peptide-based proteomic data are generated and leveraged by integrating experimentation with automation, computational approaches, and artificial intelligence/machine learning (AI/ML)-enabled tools to accelerate learning and generate high-quality datasets that can be integrated across experiments and data modalities.

Requirements

• Ph.D. in analytical chemistry, biochemistry, molecular biology, immunology, or a related discipline.
• At least 5 years of post-Ph.D. experience in mass spectrometry, preferably in an industry setting, with a demonstrated track record of developing and applying LC-MS-based proteomics approaches to address complex biological questions and advance research programs.
• Deep hands-on expertise in LC-MS analysis of biological samples, including protein extraction and digestion, peptide cleanup and separation, instrument operation, LC-MS acquisition method development, and data analysis.
• Deep expertise in discovery and quantitative bottom-up proteomics, including DDA, DIA, and targeted acquisition approaches such as PRM.
• Demonstrated ability to troubleshoot complex challenges across sample preparation, chromatography, instrumentation, data acquisition, and data analysis.
• Experience leading and developing direct reports, including setting priorities, providing actionable feedback, supporting professional development, and ensuring high-quality scientific execution.
• Experience communicating scientific findings, analyses, and recommendations to internal scientific and cross-functional teams through technical reports, presentations, and other written or verbal forums.
• Expertise with bioinformatics tools and workflows for mass spectrometry data analysis, including FragPipe, Spectronaut, Skyline, or comparable software.
• Demonstrated ability to independently define scientific approaches, challenge existing methods, and develop or implement novel solutions to complex scientific problems.

Nice To Haves

• Experience with additional mass spectrometry applications, including intact protein analysis, PTM characterization, and alternative fragmentation strategies.
• Experience with immunopeptidomics or other mass spectrometry approaches relevant to infectious disease or oncology.
• Familiarity with Bruker and Thermo Fisher Scientific mass spectrometry platforms.
• Experience using R, Python, or related programming languages for data analysis and visualization.
• Track record of introducing new mass spectrometry capabilities, technologies, or workflows into a research environment.
• Experience applying automation, computational, and AI/ML approaches to transform analytical workflows or enable new scientific capabilities.
• A desire to make an impact as part of a transformational company that is Bold, Relentless, Curious, and Collaborative.

Responsibilities

• Maintain a strong hands-on laboratory presence by designing and executing LC-MS proteomics studies and developing workflows from protein extraction and digestion through peptide separation, LC-MS data acquisition, and data analysis.
• Use LC-MS-based proteomics to address complex biological questions and partner with research teams to generate insights that inform program decisions.
• Identify scientific and technical risks, communicate limitations, and develop practical mitigation strategies.
• Manage and develop a small scientific team, setting priorities, allocating resources, and supporting high-quality scientific execution.
• Establish and maintain best practices for data quality, reproducibility, system performance, and experimental controls.
• Serve as a subject matter expert in mass spectrometry and help shape scientific approaches across research programs.
• Mentor colleagues across the broader Mass Spectrometry team and foster a culture of scientific curiosity, hypothesis-driven experimentation, and continuous improvement.
• Communicate scientific strategies, results, and recommendations through discussions, presentations, and reports.
• Evaluate and apply emerging technologies in mass spectrometry, automation, computation, AI/ML, and instrumentation to improve capability, robustness, throughput, and scientific insight.

Benefits

• Competitive healthcare, plus voluntary benefit programs to support your unique needs
• A holistic approach to well-being, with access to fitness, mindfulness, and mental health support
• Family planning benefits, including fertility, adoption, and surrogacy support
• Generous paid time off, including vacation, volunteer days, sabbatical, global recharge days, and a discretionary year-end shutdown
• Savings and investments to help you plan for the future
• Location-specific perks and extras

What This Job Offers

• Job Type: Full-time
• Career Level: Principal
• Education Level: Ph.D. or professional degree