Scientist / Senior Scientist, Bioanalytical LC–MS – Oligonucleotide

Alloy Therapeutics, Inc.; Waltham (MA); On-site; USD 126,000 - 150,000; Full time

Benefits offered by this job

401(k) company match

Generous medical, dental, and vision benefits

Unlimited PTO and flexible schedules

Annual stipend for continuing education

Wellness and Employee Assistance Program (EAP)

Job summary

Alloy Therapeutics, Inc. is seeking a hands-on scientist with expertise in LC-MS to lead the bioanalytical characterization of oligonucleotide therapeutics in Waltham, MA. This role is crucial for linking analytical data to DMPK-relevant questions to enhance drug development.

The ideal candidate will have a Ph.D. or M.S., with a strong background in LC-MS and oligonucleotide bioanalysis. Benefits include competitive compensation, unlimited PTO, and comprehensive health plans.

Qualifications

• Ph.D. or M.S. in Analytical Chemistry, Pharmaceutical Sciences, Biochemistry, or a related field.
• 3+ years (Ph.D.) or 10+ years (M.S.) of post-academic experience.
• Demonstrated experience with LC-MS and high-resolution MS oligonucleotide bioanalysis.

Responsibilities

• Develop and execute LC-MS/MS and LC-HRMS methods for oligonucleotide analysis.
• Apply LC-MS to assess oligonucleotide–protein interactions.
• Collaborate with cross-functional teams to integrate DMPK findings.
• Perform quantitative LC-MS data analysis and troubleshoot.

Skills

LC-MS/MS

Oligonucleotide exposure

Stability

Metabolism

DMPK data interpretation

Cross-functional communication

Education

Ph.D. or M.S. in Analytical Chemistry

Tools

LC-MS

High-resolution MS (HRMS)

Job description

Role Location: Waltham, MA

We are Alloy Therapeutics - a biotechnology ecosystem company empowering the global scientific community to make better medicines together. Through a community of partners, we democratize access to pre‑competitive tools, technologies, services, and company creation capabilities that are foundational for discovering and developing therapeutic biologics. The company facilitates affordable, non‑exclusive access to the entire drug discovery community from academic scientists, small and medium biotech, to the largest biopharma. At Alloy, we believe our industry should compete on getting the best drugs to patients as quickly as possible, not exclusive access to the best platforms. As a reflection of our relentless commitment to the scientific community, we reinvest 100% of our revenue in innovation and access to innovation. MAY THE BEST DRUG WIN.

Alloy has evolved from a startup into a global biotechnology infrastructure company operating 11 divisions across 5 research sites in 4 countries on 3 continents. Our model - Integrated Independence - combines centralized capabilities with entrepreneurial operating divisions. Successful members thrive in our shared culture of accountability, deliberate trust, and open communication. As a team we aspire to work together to exceed expectations and collectively contribute across the global organization to always maintain our nimble, startup culture.

At Alloy, we have an ethos of 'Mentorship-By-Apprenticeship' in all of our positions. We strive to have workers in the office when needed to interact organically and face‑to‑face. Of course, as a lab‑based operation, our cells and animals grow 7 days a week, 365 days per year. We respect and value our colleagues for their hard work that requires them to be in the lab every day. We ask our people who have more flexible accommodations, like this position, to appreciate their colleagues who have less flexibility. We are all one team!

The Role

We are seeking a hands‑on scientist with strong expertise in LC‑MS to lead bioanalytical characterization of oligonucleotide therapeutics, focusing on DMPK and biological interpretation. This LC‑MS‑focused role involves generating and interpreting data on oligonucleotide exposure, stability, metabolism, protein binding, and structural integrity to answer DMPK‑relevant questions and link analytical findings with PK/PD and biological activity.

Key Responsibilities

• LC‑MS–Driven Bioanalysis: Develop and execute LC‑MS/MS and LC‑HRMS methods for quantitative and structural analysis of oligonucleotides in biological matrices. Design and perform stability, degradation, and Metabolite Identification (MetID) studies to support DMPK. Provide a higher throughput or automated protein binding data (LC‑MS Proteomics).
• Exposure & Disposition: Apply LC‑MS and other methods to assess oligonucleotide–protein interactions, binding, and disposition, interpreting how stability, metabolism, and chemical modifications influence systemic and tissue exposure.
• DMPK & Biological Integration: Interpret LC‑MS data within a DMPK context, collaborating with cross‑functional teams to link findings with PK, PD, and biological readouts (e.g., target knockdown, gene expression).
• Data Analysis & Communication: Perform quantitative LC‑MS data analysis, troubleshoot analytical issues, and clearly communicate analytical and DMPK insights to inform decision‑making.

Required Qualifications

• Ph.D. or M.S. in Analytical Chemistry, Pharmaceutical Sciences, Biochemistry, or a related field.
• 3+ years (Ph.D.) or 10+ years (M.S.) of post‑academic experience.
• Demonstrated experience with LC‑MS and high‑resolution MS (HRMS) oligonucleotide bioanalysis, including stability, MetID, and protein binding studies.
• Comfort working cross‑functionally in a discovery environment.

Preferred Qualifications

• Experience with chemically modified oligonucleotides and/or conjugates.
• Ability to interpret LC‑MS data in a DMPK and biological context.
• Exposure to PK/PD concepts and molecular biology‑based analytical technologies (e.g., qPCR, ddPCR).

Key Skills & Competencies

• LC‑MS/MS and LC‑HRMS (core expertise).
• Oligonucleotide exposure, stability, metabolism, and protein binding.
• DMPK‑relevant data interpretation.
• Strong troubleshooting ability and scientific judgment.
• Clear cross‑functional communication.

Benefits

• Competitive base and equity compensation commensurate with level of experience and independence.
• 401(k) company match.
• Generous personal and family medical, dental and vision benefits with 100% of premiums and deductibles covered.
• Company‑paid disability (STD, LTD) and life insurance.Paid parental leave.
• Family planning support up to $45,000 (e.g., IVF/PGT, adoption, surrogacy, egg retrieval).
• Unlimited PTO and flexible schedules.
• Annual stipend for continuing education with commitment to your career through individualized professional development plan.
• Wellness and extensive Employee Assistance Program (EAP) including resources for mental wellness.

Pay Transparency

For this role, the estimated annual base salary range is $126,000 – $150,000, with the final offer based on factors such as your experience, skills, and alignment with our needs. Additionally, this role is eligible for equity compensation.

Equal Opportunity Statement

Alloy Therapeutics is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, national origin, sex, sexual orientation, gender identity, veteran status, disability, or other legally protected status. If you are unable to submit an application because of incompatible assistive technology or a disability, please contact [e-mail]. We will make every effort to respond to your request for disability assistance as soon as possible.