Senior Scientist, Proteomics

Flagship PioneeringCambridge, MA
Onsite

About The Position

Expedition Medicines is seeking a motivated and innovative Senior Scientist, Proteomics to join their 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.

Requirements

  • 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
  • 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, ProteomeDiscoverer, Spectronaut, MaxQuant)
  • Strong understanding of experimental design, assay optimization, reproducibility, and quantitative data interpretation
  • Excellent communication and cross-functional collaboration skills
  • Demonstrated ability to work independently and manage multiple priorities in a fast-paced environment

Nice To Haves

  • Experience with peptide mapping and/or intact mass spectrometry is preferred
  • Experience with laboratory automation platforms (e.g., Hamilton, Agilent Bravo) is a plus

Responsibilities

  • 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

Benefits

  • healthcare coverage
  • annual incentive program
  • retirement benefits
  • a broad range of other benefits
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