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 (or Principle Scientist), Computational Proteomics / Proteogenomics. This individual will be responsible for the development of novel analysis strategies for large-scale proteomic datasets in order to identify non-canonical proteins. The ideal candidate has a strong scientific foundation in large-scale mass spectrometry data analysis and has experience in computational workflow development. 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 novel analysis strategies for large-scale mass spectrometry data (for publicly available data and in-house generated, DDA & DIA)
• Automate our computational proteomcis workflow
• Lead our biomarker discovery efforts
• Develop computational methods to overcome analytical challenges inherent for the detection of non-canonical proteins
• Research and implement novel algorithms for analysis of large-scale proteomics datasets
• Develop and maintain software pipelines for the processing, visualization, and analysis of proteomics data (e.g., mass spectrometry, immunoaffinity assays, etc.)
• Work closely with molecular and cell biologists to collaboratively iterate on experiments in both the wet and dry lab.

Minimum Qualifications:

• PhD or equivalent experience in a relevant field like computational biology & proteomics
• 4+ years of industry experience working with developing large-scale proteomics analysis tools
• Experience integrating proteomics and genomics datasets (e.g., proteogenomics).
• Expert-level in implementing novel software solutions to analyze publicly available datasets
• Experience in developing and implementing computational algorithms and pipelines for the processing of proteomics data.
• Experienced in statistical analysis of large-scale proteomic datasets
• Excellent communication and teamwork skills.

Preferred Qualifications:

• Familiarity with proteomic instrumentation, especially for DIA-based LC-MS/MS methodologies.
• Experienced in developing or applying HLA immunopeptidomics workflows to identify and quantify MHC bound peptides
• 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 a collaborative software engineering environment, including the use of automated testing, version control, and deployment systems to reproduce and accelerate research.
• Experience using statistics and machine learning to provide analyses of complex mass spectrometry datasets to facilitate novel protein identification.
• Robust mathematical and statistical skills, and a track record of applying them to complex and noisy biological data.