Scientist​/Senior Scientist, Bioanalytical LC–MS – Oligonucleotide

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!

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.

• 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.

• 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.

• 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).

• LC‑MS/MS and LC‑HRMS (core expertise).
• Oligonucleotide exposure,…