Senior Scientist, Proteomics

Flagship Pioneering, Inc.•Cambridge, MA

1d•$126,000 - $159,500•Onsite

About The Position

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.

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