Scientist, Metabolomics

Alnylam Pharmaceuticals; Cambridge (MA); On-site; USD 110,400 - 165,600; Full time

Job summary

Alnylam Pharmaceuticals in Cambridge, MA is seeking a Metabolomics Scientist to join the Translational Research group. The role emphasizes LC-MS/MS based omics, biomarker discovery, and pharmacodynamic studies for RNAi therapeutics.

The successful candidate will design methods for endogenous metabolites and collaborate with preclinical and clinical teams. The candidate should have a PhD or equivalent with post‑doc experience, strong LC‑MS/MS expertise, and programming skills in Python or R.

Qualifications

• Experience with LC‑MS/MS methods for endogenous metabolites and lipids.
• Experience preparing samples from biofluids, tissues, or cultured cells.
• Strong publications and cross-disciplinary collaboration.

Responsibilities

• Design, validate, and apply LC‑MS/MS methods for endogenous metabolite and lipid quantification.
• Perform end‑to‑end metabolite/lipid sample preparation for biofluids, 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.
• Maintain QC records, analyze data, and document protocols/results.
• Collaborate with cross‑disciplinary and external teams to support drug discovery activities.
• Contribute to study design and biomarker strategies for programs.
• Serve as subject matter expert for translational biology questions.
• Present results and author findings in reports/manuscripts.

Skills

LC-MS/MS operation

Bioinformatics tools

Programming: Python or R

Endogenous metabolite quantification

Data analysis

Independent and teamwork

Education

PhD in analytical chemistry or related field

MS with 8+ years pharma/biotech experience

Tools

Sciex QTRAP

Thermo 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.

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 our 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 to be 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.