Company Summary:

FL69 Inc. is a privately held, early-stage biotechnology company with the vision to revolutionize the human therapeutic landscape. FL69 Inc. was founded by Flagship Pioneering, a team of entrepreneurial scientists that conceives, creates, resources, and grows first-in-category life sciences companies. Since 2000, Flagship has created over 75 groundbreaking companies that are pioneering novel and proprietary biological, industrial, and engineering approaches to solve major needs in human health and sustainability. These companies include Moderna Therapeutics (NASDAQ:MRNA), Seres Therapeutics (MCRB), Syros Pharmaceuticals (SYRS), Rubius Therapeutics (RUBY), Evelo Biosciences (EVLO), Kaleido Biosciences (KLDO), and Indigo Agriculture. FL69 Inc. is a highly dynamic, entrepreneurial, and innovation-driven organization seeking to hire an exceptional scientist to join our team.

Position Summary:

FL69 is seeking a highly motivated and team-oriented candidate for a (Senior) Scientist, Proteomics. This individual will be responsible for the discovery and analysis of non-canonical proteins in large-scale proteomic datasets. The ideal candidate has a strong scientific foundation in proteomics and a demonstrated ability to develop tailored biochemical enrichment methods. The candidate will be able to automate sample preparations. The candidate will work closely with genomics scientists, computational biologists, and a functional genomics team to identify novel targets involved in disease and bring them to preclinical models.

Key Responsibilities:

  • Develop our proteomics sample preparation workflows from cultured cells, clinical samples tissues & biofluids
  • Capable of developing novel biochemical enrichment strategies for target protein groups
  • Develop our biomarker discovery efforts
  • Automate our sample preparation steps to increase throughput
  • Manage projects in collaboration with proteomics CROs
  • Work closely with molecular and cell biologists to collaboratively iterate on experiments in both the wet and dry lab.

Minimum Qualifications:

  • PhD in proteomics or related field
  • 2+ years of industry experience (or relevant post-doc experience) developing large-scale proteomics analysis tools
  • Expert-level understanding of LC-MS/MS proteomic workflows for discovery and targeted proteomics
  • Demonstrated expertise in DDA & DIA proteomics
  • Demonstrated experience in maintaining and running mass spectrometers
  • Ability to work in a team
  • Excellent oral and written communication skills

Preferred Qualifications:

  • Experience in proteomic analysis of biofluids (urine, CSF or plasma) is a plus
  • Experience in cell-culture is a plus
  • Familiarity with top-down proteomics datasets
  • Broad understanding of LC-MS based proteomics tools used for visualization and data interpretation, e..g., OpenMS, TPP, MaxQuant, MS-GF+, X!Tandem, etc.
  • Experience in MHC immunopeptidomics or proteogenomics preferred
  • Experience in sample preparation for PPI proteomics preferred
  • Experience with SEC (size exclusion chromatography) preferred


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.

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