Quantum-Si (QSI 7.55%), a developer of next-generation protein sequencing technology, reported its Q2 2025 earnings on August 5, 2025. The most significant news was a steep revenue shortfall, as GAAP sales came in at $0.59 million compared to analyst estimates of $1.11 million—a miss of nearly 46.7%. Earnings per share (EPS, GAAP) registered at $(0.16), in line with last year’s second quarter. Despite this, the period brought gross margin gains and ongoing investment in product innovation. The overall results highlight continued struggles with commercial traction, particularly in U.S. academic markets, while the company maintains a strong cash position after a direct offering.
| Metric | Q2 2025 | Q2 2025 Estimate | Q2 2024 | Y/Y Change |
|---|---|---|---|---|
| EPS (GAAP) | $(0.16) | $(0.14) | $(0.16) | 0.0% |
| Revenue (GAAP) | $0.59 million | $1.11 million | $0.62 million | (5.0%) |
| Gross Margin | 59% | 57% | 2.0 pp | |
| Adjusted Total Operating Expenses | $23.8 million | $24.4 million | (2.5%) | |
| Adjusted EBITDA | $(22.2) million | $(22.6) million | 1.8% |
Source: Analyst estimates for the quarter provided by FactSet.
About Quantum-Si: Business overview and recent focus
Quantum-Si is a protein sequencing technology company focused on research applications. Its goal is to make protein analysis more scalable, precise, and cost-effective, using single-molecule sequencing at the amino acid level. The firm’s main platform aims to improve upon traditional tools like mass spectrometry, which can be complex and expensive.
In recent quarters, Quantum-Si has focused on growing its commercial footprint through its Platinum and Platinum Pro instruments, while maintaining a pipeline of innovation. The company is actively pursuing the launch of its Proteus platform, an advanced sequencing product aimed to enhance output and automation. Key success factors include the ability to turn innovation into real revenue, expanding into non-U.S. and non-academic customer segments, and closely managing costs in the face of persistent net losses.
Quarterly highlights: Financial and operational review
GAAP revenue for the second quarter came in well below consensus estimates. Sales (GAAP) totaled $0.59 million. GAAP revenue declined 29.8% sequentially compared to Q1 2025. U.S. academic institutions comprise roughly 20% of account placements—a segment hit hardest by these constraints, based on company disclosures from Q1 2025.
International business provided some cushioning, with about 60% of the installed base now outside the United States. The company expanded its international distributor network to 23 partners, up from 18 as of Q1 2025. Management has largely completed that expansion, shifting attention to peer-to-peer academic engagement and the launch of “expanded instrument acquisition options” to help laboratories acquire equipment amid tighter capital budgets.
Gross margin (GAAP) improved to 59%, up from 57% in the prior year quarter. This metric, which represents gross profit as a percentage of sales (GAAP), can be volatile for early-stage companies like Quantum-Si because the mix of instrument and consumable sales impacts the ratio. Management signaled that gross margin may fluctuate in the near term due to product and sales mix, as noted this quarter.
Despite some operational discipline, operating costs remain high. Adjusted total operating expenses were $23.8 million, down approximately 2.5% from last year, but GAAP net loss deepened to $28.8 million, up from $23.1 million in Q2 2024. A legal settlement charge of $3.4 million pushed costs higher. Adjusted EBITDA, a measure of operating performance that strips out some non-cash or one-time items, was negative $22.2 million. The company’s accumulated deficit (GAAP) increased to $644.7 million as of June 30, 2025.
From a product perspective, Quantum-Si continues to invest in innovation. The Proteus platform—a next-generation sequencing system—remains scheduled for a prototype by late 2025, with commercial launch in the second half of 2026. Alongside Proteus, the Version 4 Sequencing Kit (a consumable kit that enables protein analysis) is expected to launch in Q3 2025, with a new Version 3 Library Preparation Kit expected late in the year. Library prep kits help users prepare protein samples for analysis and are important for expanding the platform’s potential uses.
To support market awareness, the company has increased its academic outreach via webinars and user groups. This strategy is designed to seed adoption and generate scientific publications that could drive demand. The company reported some encouraging trends, including recurring consumable purchases from existing customers and further validation of its core technology’s utility beyond protein sequencing, such as post-translational modification studies.
Quantum-Si’s product revenue dominates sales, making up nearly all the reported figure, with service revenue a minor contributor. The company’s intellectual property portfolio—which includes nearly 400 issued patents and close to 600 pending—serves as a competitive moat, and management reports prudent allocation of research and development resources to maintain its technical lead while watching cash use closely.
One-time costs this quarter included the legal settlement mentioned above and $0.19 million in restructuring expenses. The firm raised an additional $50 million after the quarter through a direct stock offering, which, along with existing balances, should fund operations into the second quarter of 2028—offering breathing room but not eliminating the need to eventually ramp sales and reduce cash burn.
Forward outlook and what to watch
Management did not provide explicit revenue or profit guidance for the coming quarter or year, citing ongoing uncertainty, particularly as NIH funding delays persist and major revenue streams remain unpredictable. Instead, the focus remains on meeting operating expense and cash use targets for fiscal 2025: adjusted operating expenses of $103 million or less and total cash usage of $95 million or less.
Looking ahead, key issues for investors will be the pace of commercial adoption outside U.S. academic markets, recurring consumable sales that signal instrument utilization, and progress toward the major product launches that underpin future growth. The updated cash runway relieves imminent financial risk, but sustained losses will require a clear path to sales growth over the next two years. QSI does not currently pay a dividend.
Revenue and net income presented using U.S. generally accepted accounting principles (GAAP) unless otherwise noted.
