Principal Scientist, Mass Spectrometry

Moderna Therapeutics; Cambridge (MA); On-site; USD 143,000 - 257,000; Full time

Benefits offered by this job

Competitive healthcare

Well-being resources

Family planning benefits

Generous paid time off

Savings and investments

Location-specific perks

Bonus/equity eligibility

Job summary

Moderna is seeking a Principal Scientist, Mass Spectrometry to lead hands-on LC-MS proteomics within the CVBR team and drive scalable analytical capabilities for preclinical programs.

The role blends experimental leadership with cross-functional collaboration, mentoring a small team, and shaping data quality practices while advancing AI/ML-enabled approaches to generate high-quality datasets across experiments.

Qualifications

• Ph.D. in analytical chemistry, biochemistry, molecular biology, immunology, or related discipline.
• 5+ years post-Ph.D. mass spectrometry experience with LC-MS-based proteomics.
• Hands-on LC-MS analysis including protein extraction, digestion, peptide cleanup and separation.
• Experience with discovery and quantitative bottom-up proteomics (DDA/DIA/PRM).
• Experience leading and developing direct reports and cross-functional communication.
• Experience with bioinformatics workflows for MS data analysis (FragPipe/Spectronaut/Skyline).
• Ability to define scientific approaches and implement novel solutions.
• Ability to define scientific approaches and innovate.

Responsibilities

• Design and execute LC-MS proteomics studies from extraction to data analysis.
• Collaborate with research teams to generate insights informing program decisions.
• Identify risks, communicate limitations, and mitigate them.
• Lead and develop a small scientific team and allocate resources.
• Establish best practices for data quality, reproducibility, and controls.
• Serve as SME in mass spectrometry and shape scientific approaches across programs.
• Mentor colleagues and foster curiosity and improvement.
• Communicate strategies and results through discussions and reports.
• Evaluate emerging technologies in MS, automation, computation, and AI/ML.

Skills

LC-MS proteomics

Mass spectrometry

Team leadership

Data analysis

Experimental design

AI/ML in MS

Education

Ph.D. in analytical chemistry / biochemistry / molecular biology

Tools

FragPipe

Spectronaut

Skyline

Bruker / Thermo platforms

Python

Job description

The Role 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.

Here’s What You’ll Do

• 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.

Here’s What You’ll Bring to the Table (Basic Qualifications)

• 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.

Here’s What You’ll Bring to the Table (Preferred Qualifications)

• 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.

Our Working Model

As we build our company, we have always believed that an in-person culture is critical to our success. This role is 100% onsite, reflecting the importance of being physically present to support the work, collaborate closely with colleagues, and contribute to our site-based operations. Working onsite enables real-time collaboration, strong team connections, direct mentorship, and the hands-on partnership needed to deliver our mission. Join us in shaping a world where every interaction is an opportunity to learn, contribute, and make a meaningful impact. Moderna is a smoke-free, alcohol-free, and drug-free work environment.

Pay & Benefits

At Moderna, we believe that when you feel your best, you can do your best work. That’s why our benefits and well-being resources are designed to support you—at work, at home, and everywhere in between.

• 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
• The salary range for this role is $142,500.00 - $256,500.00. This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting.
• An individual’s position within the salary range will be based on several factors including, but not limited to, specific competencies, relevant education, qualifications, certifications, experience, skills, performance, and business or organizational needs.
• The successful candidate may be eligible for an annual discretionary bonus, other incentive compensation, or equity award, subject to company plan eligibility criteria and individual performance.

About Moderna

Since our founding in 2010, we have aspired to build the leading mRNA technology platform, the infrastructure to reimagine how medicines are created and delivered, and a world-class team. We believe in giving our people a platform to change medicine and an opportunity to change the world. By living our mission, values, and mindsets every day, our people are the driving force behind our scientific progress and our culture. Together, we are creating a culture of belonging and building an organization that cares deeply for our patients, our employees, the environment, and our communities. We are proud to have been recognized as a Science Magazine Top Biopharma Employer, a Fast Company Best Workplace for Innovators, and a Great Place to Work in the U.S.

Equal Opportunities

Moderna is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry or citizenship, ethnicity, disability, military or protected veteran status, genetic information, sexual orientation, marital or familial status, or any other personal characteristic protected under applicable law. Moderna is a place where everyone can grow.

Moderna is an E-Verify Employer in the United States. We consider qualified applicants regardless of criminal histories, consistent with legal requirements.

Accommodations

We’re focused on attracting, retaining, developing, and advancing our employees. By cultivating a workplace that values diverse experiences, backgrounds, and ideas, we create an environment where every employee can contribute their best. Moderna is committed to offering reasonable accommodations to qualified job applicants with disabilities. Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should contact the Accommodations team at [e-mail].

Export Control Notice

This position may involve access to technology or data that is subject to U.S. export control laws, including the Export Administration Regulations (EAR). As such, employment is contingent upon the applicant’s ability to access export-controlled information in accordance with U.S. law. Due to the nature of the work and regulatory requirements, only individuals who qualify as U.S. persons (citizens, permanent residents, asylees, or refugees) are eligible for this position. For this role Moderna is unable to sponsor non-U.S. persons to apply for an export control license.

Our Mission and Vision

At Moderna we are pioneering the development of a new class of drugs made of messenger RNA (mRNA). This novel drug platform builds on the discovery that modified mRNA can direct the body’s cellular machinery to produce nearly any protein of interest, from native proteins to antibodies and other entirely novel protein constructs that can have therapeutic activity inside and outside of cells. We have a clear mission to propel the field of mRNA science forward and deliver new medicines to patients and a unique vision for how to achieve this mission. Our Mission: To deliver on the promise of transformative messenger RNA (mRNA) science to bring new medicines to patients. Our Vision: To unlock the potential of mRNA by establishing an ecosystem of teams and partners that will work together to develop the broadest possible array of drugs, across diverse therapeutic areas and routes of administration, for serious diseases that are not treatable today.

Reasonable Accommodation Notice

Moderna will make reasonable accommodations for qualified individuals with known disabilities, in accordance with applicable law. Applicants with disabilities may be entitled to reasonable accommodation under the terms of the Americans with Disabilities Act and certain state or local laws. Please inform the company's personnel representative by calling 617-460-9346 or emailing [e-mail] if you need assistance completing any forms or to otherwise participate in the application process. Examples of reasonable accommodation include making a change to the application process or work procedures, providing documents in an alternate format, using a sign language interpreter, or using specialized equipment.