Flagship Pioneering

Senior Scientist, Proteomics

Flagship Pioneering$126K — $159K *
Pharmaceuticals & Biotech
Less than 5 years of experience
Job Overview by Ladders

Qualifications

  • Ph.D. in analytical chemistry, chemical biology, or related field with 4+ years of industry experience, or M.S. with 6+ years of experience
  • Hands-on experience with mass spectrometry-based proteomics workflows
  • Familiarity with quantitative proteomics methods such as TMT, DIA, or PRM
  • Experience with targeted chemoproteomics and peptide mapping
  • Proficiency in programming languages like Python or R for data analysis
  • Expert knowledge of proteomics data analysis software
  • Strong experimental design and reproducibility skills

Responsibilities

  • Operate and maintain advanced LC-MS instruments, specifically Orbitrap Tribrid platforms
  • Develop and execute workflows for targeted chemoproteomics
  • Design scalable protocols for high-throughput proteomics applications
  • Analyze and interpret extensive proteomics datasets systematically
  • Collaborate with cross-functional teams to drive project decisions
  • Implement innovative technologies to enhance existing proteomics methods
  • Communicate technical findings across multiple teams

Benefits

  • Healthcare coverage
  • Annual incentive program
  • Retirement benefits
  • Broad range of additional benefits
Full Job Description
THE ROLE

Expedition is seeking a motivated and innovative SeniorScientist, 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.

KEY 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

PROFESSIONAL EXPERIENCE & QUALIFICATIONS
  • 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, ProteomeDiscoverer, Spectronaut, MaxQuant)
  • 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

The salary range for this role is $126,000 - $159,500. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Expedition Medicines currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Expedition Medicines's good faith estimate as of the date of publication and may be modified in the future.

About Flagship Pioneering

Flagship Pioneering is a life sciences innovation enterprise that conceives, creates, resources, and develops first-in-category life sciences companies. The firm operates through its Flagship Labs unit, which is a dedicated innovation foundry that invents and launches transformative companies. Flagship Pioneering has created over 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents. The firm's portfolio includes companies in the fields of therapeutics, health technologies, and sustainability. Flagship Pioneering was founded in 2000 and is headquartered in Cambridge, Massachusetts.
Learn more about Flagship Pioneering
Size
500 employees
Industry

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