ProFound Therapeutics, Inc Boston, MA Scientist, Proteomic Bioinformatics

Pro Found 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.

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, tims
  
  TOF, 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 Frag Pipe, DIA-NN, Spectronaut/Spectromine, Skyline.
• Strong programming experience in Python and R for scientific computing, statistics, and visualization (e.g., Num Py, pandas, Sci Py, 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.

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort working in and contributing to a dynamic and cross‑functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidate.

We recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID‑19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship  .

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