Quantum-Si Q3 Earnings Call Highlights

Key Points

• Q3 revenue fell to $212,000 from $552,000 a year earlier, while net loss narrowed to $22.3 million from $35.7 million. Quantum-Si reiterated its approximately $1 million full-year revenue outlook and expects restructuring to deliver about $12 million in annualized savings.
• Quantum-Si remains on track to launch its Proteus protein sequencing platform in Q2 2027. Developmental testing showed about 30 times more sequencing output per chamber than Platinum Pro and a lower false discovery rate, though the company cautioned the data are not from a fully optimized final product.
• The company lowered its 2026 adjusted operating expense and cash-use outlook to $87 million or less for each, and said its $149.4 million in cash and marketable securities should fund operations into Q4 2028. Longer lead times for some components are prompting earlier orders, but management does not currently expect supply constraints to delay launch.

Quantum-Si NASDAQ: QSI reported lower third-quarter revenue and narrowed its net loss as it prepared for the planned second-quarter 2027 commercial launch of its Proteus protein sequencing platform.

The company reiterated its full-year revenue guidance of approximately $1 million and lowered its outlook for both adjusted operating expenses and cash usage. Management said restructuring actions implemented after their announcement in August are expected to generate approximately $12 million in annualized operating expense savings.

Revenue for the quarter ended September 30 fell to $212,000 from $552,000 a year earlier. Chief Financial Officer Jeff Keyes said results reflected limited near-term capital purchases of the company’s existing Platinum platform, customer awareness of the anticipated Proteus launch and commercial decisions intended to help customers transition to the new system.

Net loss narrowed to $22.3 million from $35.7 million in the prior-year quarter. Adjusted EBITDA was negative $17 million, compared with negative $20.1 million a year earlier.

Proteus Development and Pre-Orders

President and CEO Jeff Hawkins said Quantum-Si remains on track to launch Proteus in the second quarter of 2027. The company added an integrated instrument design cycle after identifying variability earlier in development, and Hawkins said recent performance data indicated those issues had been substantially addressed.

Design activities for the additional cycle are complete, major components have been ordered and subassemblies are being manufactured, he said. The first instruments from that build are expected during the current quarter, but Hawkins clarified during the analyst question-and-answer session that they are intended for research and development rather than sale.

Quantum-Si has also started a Proteus pre-order program. Hawkins said customers placing an order with a deposit can receive preferred pricing and priority access when early access or commercial placements begin. He said the company could provide visibility into pre-orders in early 2027 and expects to place a couple of machines at customer sites for early-access work.

Since launching a Proteus roadshow in April, the company has held events in more than 35 cities and reached more than 800 attendees across the United States, Canada and Europe, Hawkins said. He described prospective customer interest as a relatively even mix of existing users and new accounts.

Sequencing Progress

Hawkins said Quantum-Si has demonstrated detection of 19 amino acids and expects to demonstrate detection of the 20th before the end of 2026. Its commercially available sequencing kit supported 15 amino acids at the end of 2025, while an 18-amino-acid developmental kit was used to generate data presented at the World HUPO conference in September.

The CEO distinguished between demonstrating detection in a research formulation and incorporating it into a kit. He said the company had not decided whether to develop a 19-amino-acid kit or wait to include the 20th, but felt it was in a strong position to have all 20 available at the Proteus launch if the remaining detection milestone is achieved.

In the interim World HUPO study, developmental Proteus equipment produced approximately 30 times more sequencing output per chamber than Platinum Pro, Hawkins said. Proteus recorded a 1.36% false discovery rate versus 6.58% for Platinum Pro and identified all proteins in 10-plex and 24-plex reference mixtures.

Hawkins cautioned that the conference data did not represent a fully optimized final product. He said Quantum-Si expects to provide definitive performance specifications at launch and anticipates further improvement in several measures, including peptide identification and sample complexity.

The company is also incorporating artificial intelligence and machine learning into its analysis pipeline. Hawkins said the combination of AI-driven analysis and detection of all 20 amino acids could provide a path toward reference-free sequencing in 2027, though the work remains in development.

Spending Outlook and Supply Chain

Quantum-Si lowered its 2026 adjusted operating expense guidance to $87 million or less from $98 million or less. It also reduced its total cash usage outlook to $87 million or less from $93 million or less.

Third-quarter GAAP operating expenses declined to $23.9 million from $40 million a year earlier, a period that included net lease termination and legal settlement expenses. Adjusted operating expenses fell to $18.2 million from $21.4 million.

The company held $149.4 million in cash equivalents and marketable securities at September 30. Keyes said Quantum-Si believes it has sufficient capital to fund operations into the fourth quarter of 2028, including the activities required for the Proteus launch.

Keyes said AI-related demand has lengthened lead times for some Proteus components. To address the risk, Quantum-Si is ordering parts earlier, committing volume with suppliers and, where practical, qualifying second sources and building safety stock. The purchases may modestly increase near-term working capital needs, he said, but are included in the cash outlook.

Based on current information, Keyes said, the company does not expect supply chain conditions to affect the planned second-quarter 2027 launch.

About Quantum-Si (NASDAQ:QSI)

Quantum-Si Incorporated NASDAQ: QSI is a life sciences technology company focused on transforming protein analysis through next-generation proteomics. The company develops tools designed to identify and characterize proteins at the single-molecule level, with potential applications in drug discovery, translational research, diagnostics development and precision medicine.

Its primary offering is the Platinum platform, which combines a benchtop sequencing instrument, semiconductor-based technology, consumables and data-analysis software.

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