Scientist, Metabolomics

Alnylam Pharmaceuticals, Inc.; United States; On-site; USD 110,400 - 165,600; Full time

Job summary

Alnylam Pharmaceuticals, Inc. is seeking a Metabolomics Scientist to join the Translational Research team in Cambridge, MA. The role focuses on untargeted and targeted LC-MS/MS workflows to support biomarker discovery and target validation for RNAi-based therapeutics.

The candidate will prepare samples, operate LC-MS/MS systems, and analyze omics data to inform pharmacodynamic activity and study design. Strong collaboration and publication record are valued; onsite work in Cambridge, MA.

Qualifications

• PhD in analytical chemistry, biochemistry, chemical engineering or related field; post-doc a plus; or MS with 8+ years pharma/biotech.
• Direct experience with triple-quadrupole and high-resolution LC-MS/MS for endogenous metabolite/lipid quantification.
• Experience with extracting metabolites from biofluids, tissues, or cultured cells.
• Familiarity with omics-based bioinformatics software; programming in Python or R is a strong plus.
• Experience with stable isotope tracing or metabolic flux analysis is a plus.
• Strong publication record and collaborative experience.
• Excellent written and oral communication; able to work independently and in teams.

Responsibilities

• Design, validate, and apply LC-MS/MS methods for endogenous metabolites and lipids.
• Prepare metabolite/lipid samples from biofluids, tissues, and cultured cells.
• Operate and troubleshoot LC-MS systems and maintain QC records.
• Develop bioinformatics tools for large-scale data processing and statistics.
• Collaborate with cross-disciplinary and external teams in drug discovery.
• Contribute to study design and biomarker strategies for programs.

Skills

LC-MS/MS operation

Method development

Sample preparation

Bioinformatics

Python or R

Isotope tracing

Scientific communication

Team collaboration

Education

PhD in analytical chemistry or related field

Tools

LC-MS instruments (QTRAP/Orbitrap)

Job description

Overview

Alnylam’s Translational Research group is seeking a highly motivated Metabolomics Scientist to join our team. We use untargeted and targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based omics and computational biology to support biomarker discovery and target validation efforts for our RNAi-based therapeutics. The successful candidate will have a background in biological sample preparation for endogenous metabolites/lipids, LC-MS/MS operation/troubleshooting, and omics-level data analysis.

This position is onsite and will be primarily located in Cambridge, MA.

Key Responsibilities

• Design, validate, and apply LC-MS/MS methods for endogenous metabolite and lipid quantification to identify and measure biomarkers, characterize pharmacodynamic activity of novel therapeutic molecules, and answer foundational biological questions.
• Perform end-to-end metabolite/lipid sample preparation protocols for biofluids, solid tissues, and cultured cells.
• Operate, maintain, and troubleshoot LC-MS systems as needed.
• Develop and apply bioinformatics tools for large-scale data processing and statistical analysis.
• Identify and onboard novel technologies for biomarker measurement and identification.
• Maintain QC records, analyze data, and document protocols/results in a clearly organized electronic lab notebook.
• Collaborate with cross-disciplinary and external teams to support preclinical and clinical drug discovery activities.
• Contribute to preclinical/clinical study design and biomarker strategies for drug candidate programs.
• Serve as subject matter expert for general questions pertaining to translational biology.
• Present results at internal/external meetings and author findings in reports/manuscripts.

Qualifications

• PhD in analytical chemistry, biochemistry, chemical engineering, biological engineering, or related field required, with post-doctoral experience a plus; or MS with 8+ years’ experience, preferably in pharma/biotech.
• Direct experience with triple-quadrupole and high-resolution accurate mass LC-MS/MS-based methods for endogenous metabolite/lipid quantification (ideally with Sciex QTRAP and Thermo Orbitrap systems), including assay development and validation.
• Experience with metabolite/lipid extraction sample preparation from biofluids, tissues, and/or cultured cells.
• Experience with relevant omics-based bioinformatics software; familiarity with basic programming languages (e.g. Python or R) and/or AI-based coding tools (e.g. Claude Code or Codex) is a strong plus.
• Experience with stable isotope tracing and/or metabolic flux analysis is also a plus.
• A strong publication record and demonstration of successful collaborations.
• Strong written and oral communication skills.
• Strong abilities to work both independently and in a team environment.

Intellectual curiosity, a passion for science, critical thinking skills, and a willingness to ask questions.

#LI-JR1

U.S. Pay Range

$110,400.00 - $165,600.00

The pay range reflects the full-time base salary range we expect to pay for this role at the time of posting. Base pay will be determined based on a number of factors including, but not limited to, relevant experience, skills, and education. This role is eligible for an annual short-term incentive award (e.g., bonus or sales incentive) and an annual long-term incentive award (e.g., equity).

Alnylam’s robust Total Rewards package is designed to support your overall health and well-being. We offer comprehensive benefits including medical, dental, and vision coverage, life and disability insurance, a lifestyle reimbursement program, flexible spending and health savings accounts and a 401(k)with a generous company match. Eligible employees enjoy paid time off, wellness days, holidays, and two company-wide recharge breaks. We also offer generous family resources and leave. Our commitment to your well-being reflects our belief that caring for your people fuels the impact we create together.

Learn more about these and additional benefits offered by Alnylam by visiting the Benefits section of the Careers website: https://www.alnylam.com/careers

About Alnylam

We are the leader in RNAi therapeutics – a revolutionary approach with the potential to transform the lives of people with rare and common diseases. Built on Nobel Prize-winning science, Alnylam has delivered the breakthroughs that made RNAi therapeutics possible and are just at the beginning of what’s possible. Our deep pipeline, late-stage programs, and bold vision reflect our core values: fierce innovation, passion for excellence, purposeful urgency, open culture and commitment to people. We’re proud of being a globally recognized top employer, where an authentic, inclusive culture and breakthrough thinking fuel one another.

At Alnylam, we commit to an inclusive recruitment process and equal employment opportunity. Qualified applicants will receive consideration for employment without regard to their sex, gender or gender identity, sexual orientation, race, color, ethnicity, national origin, ancestry, citizenship, religion, creed, physical or mental disability, pregnancy status or related conditions, genetic information, veteran or military status, marital or familial status, political affiliation, age, or any other factor protected by federal, state, or local law. Alnylam is an E-Verify Employer.