PumpkinSeed Protein Sequencing

Yesterday we looked at a new nanopore protein sequencing startup, today we look at a label-free optical approach. This gives further credence to the idea that if you have a good new sensing technology you are now more likely to see that directed to Protein sequencing than DNA sequencing.

The company in question is PumpkinSeed. The work appears to be funded by the CZI, Gates Foundation, and Moore Foundation¹ but it’s unclear what VC funding the company has received. And I assume they are seed stage.

There are a few bits and pieces floating around about the PumpkinSeed. Including this great Youtube video. There are also two published patents.

The second of these is a little more exciting to me as it discusses a label-free de novo protein sequencing approach. The approach is only briefly mentioned in their slides, but described in depth here.

At a high level the approach is very simple. They take single molecule Raman spectra of short peptides. The terminal amino acid is cleaved, then another spectra is taken² sequentially until you have Raman spectra after every cleaved amino acid.

Then you combine³ all the spectra of these incrementally shorter peptides to derive the original sequence: