Quantum-Si Brand Guidelines: Rothberg’s Protein Sequencing Chip From Connecticut

A chip-based idea from the Ion Torrent founder.

Quantum-Si was founded in 2013 by Jonathan Rothberg, the scientist and entrepreneur behind 454 Life Sciences and Ion Torrent, according to the company and to English Wikipedia. The company says Rothberg started it after Ion Torrent had shown that a benchtop instrument could open up DNA sequencing, and that its aim was to make protein sequencing accessible in the same way. It was one of the companies formed through 4Catalyzer, the startup accelerator Rothberg set up in Guilford, Connecticut, which English Wikipedia says also produced Butterfly Network and Hyperfine.

The firm’s subject is the proteome, the set of proteins expressed in a cell, and its approach rests on a semiconductor chip. GEN Edge reported in June 2021 that the company described its chip as a massively parallel single-photon counting device designed to read proteins one molecule at a time, and that it called its method Time Domain Sequencing: rather than telling amino acids apart by colour, the system measures timing. Rothberg told the magazine that chips are very precise at measuring time, which lets the system tell different amino acids apart, including modified ones.

The underlying science was set out in the journal Science in October 2022, in a paper by Quantum-Si researchers with co-authors from ESPCI Paris, Rutgers University and the University of Wollongong. It described single peptides probed in real time by a mixture of dye-labelled “recognizers” that bind the amino acid at one end of the chain, while enzymes called aminopeptidases cut the amino acids away one by one. The paper gave the company’s address as Guilford, Connecticut, and was the subject of a commentary in Nature Methods that December.

Platinum, Platinum Pro and Proteus.

Quantum-Si went public in June 2021 through a merger with HighCape Capital Acquisition, a special purpose acquisition company sponsored by the life-sciences investor HighCape Capital. GEN Edge reported that HighCape’s stockholders approved the deal on 9 June 2021 and that the combined company’s shares began trading on the Nasdaq under the symbol QSI two days later. At that point Rothberg was executive chairman and John Stark was chief executive, and the company was based in Guilford with offices in New York, San Diego and Palo Alto, the magazine said. English Wikipedia says Rothberg became interim chief executive in February 2022.

The product line named in 2021 was a platform in three parts: Platinum, a benchtop protein sequencing instrument that GEN Edge described as the size of a microwave; Carbon, an automated sample-preparation instrument; and the Quantum-Si Cloud software service, supported by reagent kits and chips. The company then said the platform was on track to launch for research use in 2022.

A second-generation instrument followed. In a release of March 2025 the company announced that it had begun shipping Platinum Pro, which it said builds on the original Platinum with an enlarged touchscreen, a choice of local or cloud-based data analysis and a “Pro Mode” for custom applications, offered through a Technology Access Program. Its website now presents Platinum and Platinum Pro as, in its words, the world’s first next-gen protein sequencing instruments, and labels its products for research use only.

The next platform is called Proteus. In November 2026 the company said it expected a commercial launch in the second quarter of 2027 and had opened a pre-order programme; the launch had not taken place at the time of writing. The same release said a reduction in force announced in August 2026 had affected about a fifth of its staff.

Instruments, chips and data.

DNA sequencing and genomics-tools companies sell to scientists, yet their pictures tend to repeat a small set of scenes: a benchtop instrument with a glowing panel in a clean, bright laboratory; a flow cell or chip held between gloved fingers; a colourful double helix or a data visualisation; a researcher studying results on a screen. Because the chemistry itself is invisible, the hardware, the consumables and the data become the main images.

Conferences are where many of these companies meet their customers. The Advances in Genome Biology and Technology meeting, known as AGBT, and the annual meeting of the American Society of Human Genetics, known as ASHG, are regular venues for news. Oxford Nanopore says it presented its first nanopore sequencing data at AGBT in February 2012, and Genetic Engineering & Biotechnology News reported in November 2024 that PacBio introduced its Vega benchtop sequencer at ASHG with a concert. Some companies run their own events too: Oxford Nanopore says it held the first London Calling conference for its users in May 2015.

Names and colours do much of the identity work. Instruments carry short, memorable product names, and some companies give their hardware one recognisable colour; GEN reported that PacBio’s new look, introduced with its Revio sequencer, came with a commitment to pink. The palettes in these guides are our own interpretations, not official colour standards.

This guide sets out what can be checked about each company — who founded it, who owns it, and which platforms it sells — and marks clearly what rests only on the company’s own word. Where a company describes its instruments as for research use only, or says they are not intended for diagnosis, as PacBio and Oxford Nanopore do, we report that as the company states it.

From Guilford to Branford.

Quantum-Si is now led by Jeff Hawkins, its president and chief executive, whose company biography lists earlier roles at Illumina, GenMark, Hologic and Abbott Laboratories. Its press releases carry a Branford, Connecticut dateline, as did its third-quarter report of November 2026, and the business trades on the Nasdaq as Quantum-Si Incorporated.

The way the company describes itself has shifted over time. Its March 2025 release called it “The Protein Sequencing Company”; its November 2026 statements describe a proteomics technology company redefining protein analysis through single-molecule protein sequencing. The website speaks of single-molecule proteomics from the benchtop, for “every lab, everywhere,” and groups its uses under headings such as protein identification, protein variants, modification analysis and protein barcoding.

The founder’s earlier companies give useful context. GEN Edge noted in 2021 that 454 Life Sciences, which Rothberg founded in 2000, was later acquired by Roche, and that Ion Torrent was bought by Life Technologies in 2010 and is now owned by Thermo Fisher Scientific. Rothberg told the magazine that Quantum-Si was the next step after those two sequencing companies, moving from DNA to proteins on a chip.

For a design guide, Quantum-Si shows how a young instrument maker can build its identity around one idea — reading proteins on a chip — and carry it through successive product names, from Platinum to Proteus. Compare Thermo Fisher, which now owns the Ion Torrent sequencing line, and PacBio, another maker of single-molecule instruments. For this guide we use a deep violet, a graphite and a pale silver with a geometric sans, an unofficial interpretation; no product or logo is reproduced.

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