Protein Sequencing-by-Subtraction with Pumpkinseed Cofounder/CEO Jen Dionne

“We right now are developing our technology to be able very soon to sequence roughly hundred-length proteins that are on each of those sensors within a 24-hour period. You can think about this as being essentially 10 billion letters per day: 100 million sensors times those 100-mers on each sensor and then sequencing letter by letter.”That’s the scale that Pumpkinseed CEO and Cofounder Jen Dionne thinks her company can reach for analyzing proteins. The technology, developed in her lab at Stanford University, uses Raman spectroscopy to fingerprint molecules and Edman degradation to achieve sequencing-by-subtraction of peptides: 30 amino acids at a time now, possibly up to 300, or full-length proteins, in the future. The ability to capture 10 billion amino acids per day would represent several orders of magnitude better throughput than the best and fastest proteomics methods available today, whether via mass spectroscopy or other single-molecule technologies being developed by competitors like Quantum-Si or Nautilus. Remarkably, that’s still a long way from achieving the data acquisition rate that state-of-the-art high-throughput sequencers can achieve, but it’s enough to start thinking about making the type of impact that the first next-generation sequencers had on biological research. Join us as we discuss the underlying physics behind Pumpkinseed’s technology, Jen’s journey from lab to C-suite, the applications they’re already pursuing, and her love of sports, including the World Cup. For more information, check out pumpkinseed.bio or email Jen. Links to papers discussed in the episode:Hu et al. Rapid genetic screening with high quality factor metasurfaces. Nature Communications, July 26, 2023.Zhang et al. From Genotype to Phenotype: Raman Spectroscopy and Machine Learning for Label-Free Single-Cell Analysis. ACS Nano, July 1, 2024.Stiber, et al. Dynamic, single-cell monitoring of CAR T cell identity and activation with Raman spectroscopy. BioRxiv, February 23, 2026.