Senior Scientist, Proteomics

Company Description

Expedition Medicines is a privately held, early‑stage biotechnology company pioneering the emerging field of Protein Editing. At Expedition Medicines we create small molecules that edit protein structure and function to unlock presently undruggable targets and a broad array of therapeutic modalities. Our platform integrates novel small‑molecule chemistry, chemoproteomic discovery technologies, and machine learning to enable generative design. Expedition Medicines is backed by Flagship Pioneering, bringing courage, vision, and resources to guide Expedition Medicines from platform validation to patient impact.

We are seeking collaborative, relentless problem solvers that share our passion for impact to join us!

Expedition is seeking a motivated and innovative Senior Scientist, Proteomics to join our team. In this role, you will play a critical role in the development and application of cutting‑edge chemoproteomics workflows to support drug discovery programs and platform innovation. The successful candidate will combine strong experimental expertise in mass spectrometry‑based proteomics with quantitative data‑analysis skills to enable biological insight and drive decision‑making across multidisciplinary discovery teams.

This individual will contribute to the advancement of a state‑of‑the‑art chemical proteomics platform supporting targeted chemoproteomics, lead‑compound characterization, and biomarker discovery efforts. The ideal candidate is highly collaborative, scientifically rigorous, and capable of independently driving projects in a fast‑paced research environment.

• Operate, maintain, and troubleshoot state‑of‑the‑art LC‑MS instrumentation, including Orbitrap Tribrid platforms with FAIMS
• Develop, optimize, and execute targeted chemoproteomics workflows to support discovery programs
• Design and improve scalable sample preparation and experimental workflows for high‑throughput proteomics applications
• Analyze and interpret large‑scale proteomics datasets using quantitative and statistical approaches
• Collaborate closely with proteomics, biology, chemistry, and computational teams to design experiments, interpret results, and guide project strategy
• Develop and implement innovative chemical proteomics technologies and methodologies to enhance platform capabilities
• Communicate findings and technical advances clearly across cross‑functional teams

• Ph.D. in analytical chemistry, chemical biology, biochemistry, or a related discipline with 4+ years of industry experience, or M.S. degree with 6+ years of industry experience
• Extensive hands‑on experience with mass spectrometry‑based proteomics workflows and instrumentation
• Experience with quantitative proteomics methods including TMT, DIA, PRM, or related approaches
• Experience with targeted chemoproteomics workflows and applications
• Experience with peptide mapping and/or intact mass spectrometry is preferred
• Proficiency in analyzing complex, large‑scale proteomics datasets using computational methods and programming languages such as Python or R
• Expert level understanding of proteomics data analysis software (e.g., MSFragger, Proteome Discoverer, Spectronaut, Max Quant)
• Strong understanding of experimental design, assay optimization, reproducibility, and quantitative data interpretation
• Experience with laboratory automation platforms (e.g., Hamilton, Agilent Bravo) is a plus
• Excellent communication and cross‑functional collaboration skills
• Demonstrated ability to work independently and manage multiple priorities in a fast‑paced environment

Location:

Cambridge, MA

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID‑19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of…