Scientist, Proteomic Bioinformatics

Flagship Pioneering-posted 1 day ago
$115,000 - $165,000/Yr
Full-time • Mid Level
Boston, MA
251-500 employees
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ABOUT PROFOUND THERAPUETICS ProFound Therapeutics is pioneering the discovery of the expanded human proteome to unlock a new universe of potential therapeutics. By integrating multi-omics, advanced computation, and translational biology, we aim to reveal and characterize thousands of previously uncharted proteins and systematically explore their role in health and disease. Summary We are seeking a highly skilled Proteomics Bioinformatician with deep expertise in computational data analysis for next-generation mass spectrometry technologies, quantitative proteomics pipelines and proteogenomics. The ideal candidate will develop, optimize, and implement workflows for processing large-scale proteomic datasets, and implement automated MS platforms.

  • Develop, implement, and maintain bioinformatics pipelines for MS-based proteomics data (i.e. DDA, DIA, PRM, ion mobility separation)
  • Integrate and analyze large-scale datasets from platforms including Orbitrap instruments, timsTOF, and next-generation DIA.
  • Build pipelines for data QC, normalization, feature alignment, identification, quantification, and downstream statistical analysis.
  • Apply and develop statistical models, machine-learning methods, and visualization tools using Python and R.
  • Automate whole data processing workflows (e.g., Nextflow) and build reproducible analysis modules.
  • Collaborate with experimental teams to refine study design, troubleshoot MS data, and interpret results.
  • Produce comprehensive, well-documented code and reports for internal and external stakeholders.
  • Stay up to date with emerging proteomics tools, algorithms, and quantitative strategies.
  • Master’s w/ 4+ YOE or PhD in Bioinformatics, Computational Biology, Proteomics, Computer Science, or a related discipline.
  • Demonstrated expertise in mass spectrometry proteomics data analysis, with experience using tools such as FragPipe, DIA-NN, Spectronaut/Spectromine, Skyline.
  • Strong programming experience in Python and R for scientific computing, statistics, and visualization (e.g., NumPy, pandas, SciPy, scikit-learn, ggplot2, dplyr, tidyverse).
  • Hands-on experience with statistical analysis, differential expressions, FDR control, PTM analysis, and high-dimensional data processing.
  • Comfortable working with large, complex datasets and high-performance or cloud computing environments.
  • Familiarity with MS data formats, prediction models and conversion tools.
  • Excellent communication skills and ability to collaborate across computational and experimental teams.
  • Proven ability to write clean, reproducible, well-documented code.
  • healthcare coverage
  • annual incentive program
  • retirement benefits
  • a broad range of other benefits
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