Invest in your career with a Madrona-funded company.


Principal Scientist, Proteomics Applications

Nautilus Biotechnology

Nautilus Biotechnology

San Carlos, CA, USA
Posted on Tuesday, June 27, 2023
At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the proteome to accelerate drug development and enable a new world of precision and personalized medicine. We are developing a single-molecule protein analysis platform of unprecedented sensitivity, scale, and ease of use that we believe will democratize access to the proteome – one of the most dynamic and valuable sources of biological insight. To accomplish this, we are pursuing deep, hard science with an entrepreneurial mindset and creating a world-class team of builders, innovators, and dreamers across a wide range of disciplines.
We are hiring for a development minded Principal Scientist, Proteomics Applications to join our Applications and Biochemistry teams. This role will work as an intermediary between our collaborative research partners and our R&D teams to ensure that application specific sample preparation workflows and analysis methods are optimized and validated for use in a variety of different study designs. This important work will serve as the foundation of studies that use our platform to investigate interesting biological questions with our external partners and customers. This scientist will need to refine and optimize baseline sample extraction, enrichment, denaturation, functionalization and bio-conjugation workflows against diverse biological targets. Validation and optimization will include the development of appropriate model systems to generate single-molecule protein-DNA conjugate libraries that integrate with the proprietary flow cells within the Nautilus Protein Analysis Platform.


  • Serve as the applications team technical expert for sample preparation and protein chemistry.
  • Optimize protein extraction, isolation, enrichment, handling, solubility, and stability for proteins and samples across various applications of interest to our collaborative partners.
  • Advise and train team members on proteomics/protein chemistry best practices to prevent chemical or enzymatic degradation of polypeptides and PTMs through application-specific bioconjugation workflows.
  • Develop SOPs and model systems for various proteomics applications.
  • Implement and develop strategies for protein extraction, isolation and enrichment from a variety of sample types including mammalian cell lysates, tissue samples, and blood.
  • Work with other team members to ensure compatibility of protein manipulation strategies with our bioconjugation chemistries.
  • Collaborate with team members to ensure compatibility of protein manipulation strategies with downstream bioconjugation chemistries.
  • Work closely with commercial team to understand and interpret customer application requirements and convert those to product and technical requirements/specifications for the R&D organization. Lead applications team in strategies to convert customer requirements into product requirements. Map technical feasibility strategies and commercial development work.


  • PhD with 10+ years of relevant industry experience with protein chemistry, extraction, purification, or proteomics sample preparation workflows is preferred.
  • Foundational expertise in proteomics, protein chemistry and/or protein biophysics.
  • Significant hands-on laboratory experience with protein manipulation, including a wide variety of proteins in the context of complex mixtures (lysates, tissue, etc.)
  • Hands-on experience with various proteomics sample preparation workflows and/or kit development, protein experience required.
  • Experience in a customer-facing role is a plus.
  • Experience working in a commercial reagents / chemistry R&D environment is a plus.

Nautilus Team Culture

  • We are curious go-getters: this is a team of life-long learners who aren’t afraid to tackle the big challenges and we embrace the journey.
  • We are detail oriented: we do great science by working smart & with diligence where we learn from our trials and mistakes.
  • We are easy to work with: we want our workplace to be one where everyone can share their perspective and be treated with respect and kindness.