From Smudge to Sequence: Quantum-Si Commercializes the First Single-Molecule Protein NGS Platform

In 2000, Jonathan Rothberg’s stealth company, 454 Life Sciences, set out to change the next-gen sequencing industry, which was just getting started. Quantum-Si Incorporated (QSI), the restless entrepreneur’s latest project, aims to do the same for peptide sequencing. The business has unveiled Platinum, the first platform for single-molecule protein sequencing of the next generation. The benchtop instrument will begin to arrive in 2023 at the beginning of the first quarter (Q1).

Jonathan Rothberg, who started QSI in 2013, told GEN Edge: “Cancer is a disease of the DNA in the genome. So next-generation DNA sequencing transformed our understanding, diagnosis, and treatment of cancer. Most complex diseases are diseases of the proteome, so QSI’s next-generation protein sequencing will be just as transformative.”

“This is the next pivot point in the biological tools space to lead to identifying new proteins that are associated with disease for clinical diagnostics or therapeutic targets,” Patrick Schneider, PhD, president and chief operating officer at QSI, told GEN Edge. “New learnings will come when we start to sequence proteins.”

A complex protein alphabet

When understanding protein function and how it relates to disease, some things are present in proteins but not encoded in DNA. The only way to access these things is to sequence the proteins. So, why is protein sequencing not already prevalent, but DNA sequencing has been for 20 years? Why are readouts of bands, smudges, and smears still the status quo for proteins?

Brian Reed, head of research at QSI, thinks that the fundamental reason is that DNA can be amplified and has a minimal four-letter alphabet. “Those two items alone dramatically simplify the technological hurdles to get DNA sequencing and to drive the cost down,” said Reed. “But protein sequencing fundamentally requires single-molecule sensitivity. There’s no PCR for proteins, and there are 20 amino acids, most of which can be modified.”

Reed says that to do biophysics experiments on a single molecule, you need a whole biophysics lab with expensive microscopes, lasers, and other types of optical instruments. This is not scalable. “We wanted to build a small bench-top device at a low price point that could democratize experimentation that required single-molecule sensitivity,” said Reed. “The sequence doesn’t lie. You know you’re getting as sensitive a measurement of that sample as is physically possible.”

The science behind Platinum

To develop Platinum, the team at QSI had to overcome several engineering hurdles. First, they had to design a new, very small, affordable laser that fits inside the instrument and works in concert with a semiconductor chip. Second, they developed a dynamic protein sequencing assay that happens in real-time and does not require any fluids or changes to the semiconductor chip.

With this technology, called Time Domain Sequencing, individual peptides are probed in real-time by a mixture of dye-labeled N-terminal amino-acid “recognizers” and simultaneously cleaved by aminopeptidases. Then, to find peptide sequences, the chip measures the fluorescence intensity and how long it lasts instead of its wavelength. Based on the kinetic signatures of recognizers, the platform can also figure out single amino-acid substitutions and changes that happen after translation. Reed and colleagues demonstrated the proof-of-concept for this sequencing by the stepwise-degradation process in a Science paper in 2022.

There’s nothing particularly new that researchers have to do when using the Platinum platform, as the sample prep workflow is similar to that for mass spectrometry. “Once you have a tube with your proteins of interest, we have a kit and a process that can be easily automated that can digest the proteins into peptide fragments, just like you would do with the same enzymes that you would use for mass spectrometry,” said Reed. “But then, instead of running those peptides on a mass spectrometer, we do a pretty quick ‘click chemistry’ reaction to modify the C terminus [of the peptide] for mobilization on the chip. Then you just load the chip, put it in the instrument, and wait for all the data to stream out!”

A new market

When asked what learnings from genome NGS were used to develop Platinum, Rothberg said, “Leverage Moore’s law and the $1 trillion that went into the semiconductor supply chain. Be first. Invest in the business to make sure you lead the market.”

In building out this new market for single-molecule protein sequencers, QSI’s commercialization approach for Platinum targets academic researchers at first. “While we have had pharmaceutical companies express an interest, we think targeting the academic folks is probably better,” said Schneider. “Our approach in the next three or four months is to see how many publications and applications we can get. I want [Platinum] to be in every figure legend, providing an orthogonal view of protein sequencing. So, there’ll be a lot of market development activity in the first half of next year.”

The goal for Platinum is not to replace optical instrumentation in biophysics labs. Instead, researchers that rely on those kinds of tools are the target. “Customers who do that kind of experimentation are excited about the possibility that one day they could be doing their experiments on this little device—it would be so much easier,” said Reed. “We see this implementation of protein sequencing as a new modality for protein science. There are multiple ways that people go about doing experiments on detecting and measuring proteins. This is a fantastic, innovative new tool that we’ll start seeing the first customers put into practice over the next year.”

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