(Sr) Scientist, Proteomics at Flagship Labs 83, a Flagship Pioneering Company

Flagship Labs 83

Pioneering a new class of medicines, Artificial Biologics

Scientist / Senior Scientist, Proteomics

What if… you could join an organization that is discovering and developing an entirely new class of medicines, one that leverages both chemistry and biology, to overcome many of the challenges faced by current therapeutics today?

Company Summary:

Flagship Labs 83, Inc. (FL83) is a privately held, early-stage biotechnology company on a mission to make biology better through chemistry. We are pioneering the development of a transformational new class of medicines, called Artificial BiologicsTM, that is unlocked by novel synthetic and computational technologies. We seek an exceptional proteomicist to join our entrepreneurial and innovation-driven organization.

FL83 was founded in Flagship Pioneering’s venture creation engine, where companies such as Moderna Therapeutics (NASDAQ: MRNA), Rubius Therapeutics (NASDAQ: RUBY) and Generate Biomedicines were conceived and created. Since Flagship’s founding in 2000, the firm has originated and fostered the development of more than 100 scientific ventures resulting in over $34 billion in aggregate value, more than 500 issued patents and more than 50 clinical trials for novel therapeutic agents.

Position Summary:

Flagship Labs 83 is looking for a creative and motivated Scientist or Senior Scientist Proteomics to build our Artificial BiologicsTM Product Development team. As part of the founding scientific team, this individual will be instrumental in building the analytical platform, using novel analysis and sequencing strategies to characterize large and complex Artificial BiologicsTM libraries, with the aim to develop impactful new therapeutics. This individual will have experience applying state-of-the-art proteomics data acquisition and analysis methods, enabling large-scale mass spectrometry data analysis and computational workflow development.  A successful candidate will be an excellent collaborator working closely with our Computational Protein Design, Chemistry, and Biology teams to implement and execute rapid design-build-test iteration cycles and optimized methods.


  • Develop and implement a novel analytical platform for discovery and characterization of peptides, proteins, and biopolymer libraries (Artificial BiologicsTM) using state-of-the-art proteomics and peptidomics approaches, from sample preparation, to acquisition and data analysis
    Conduct DDA, DIA, and PRM/MRM/SRM based proteomics studies and establish automated sequencing workflows
  • Implement diverse enrichment and sample preparation protocols for untargeted or targeted proteomics studies from varied biological samples, including cultured cells, tissues, and biofluids
  • Analyze large proteomics datasets using commercial and/or open-source packages by processing, visualizing, and quantifying multidimensional (MSn) spectral data
    Contribute to ongoing innovation within the company through the introduction of the most recent techniques and trends in proteomics and peptidomics
  • Collaborate with an entrepreneurial and interdisciplinary team to actively create, shape, and execute the vision of the company


  • PhD (or equivalent) experience in a relevant field such as analytical chemistry, biochemistry, proteomics, or computational biology
  • 3+ years of experience developing large-scale proteomics analysis tools
  • Demonstrated experience in operating and maintaining nanoLC-MS/MS instrumentation
  • Experienced in proteomics sample preparation including protein extraction, digestion and peptide separation
  • Experience using statistics (P-value, FDR) to provide analyses of complex mass spectrometry datasets to facilitate novel protein discovery and design
  • Broad understanding of proteomics database search, quantitative analysis, visualization, and interpretation, using commercial and/or open-source software, such as MaxQuant, Skyline, PEAKS, DIA-NN, Spectronaut, Spectromine, Proteome Discoverer
  • Computational skills such as bioinformatics, statistics, programing (R/Python); AWS cloud computing is a plus
  • Demonstrated ability to communicate and work effectively with a cross-disciplinary team, external contractors and members of other multifunctional teams within and outside of the Flagship Pioneering ecosystem

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

Recruitment & Staffing Agencies*: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.*

To apply for this job email your details to jdunphy@flagshippioneering.com