Unpacking the Analytical Toolbox for PFAS: From Targeted Quantitation to Unknowns

Dubbed “forever chemicals” for their extreme persistence, per- and polyfluoroalkyl substances (PFAS) resist breakdown, bioaccumulate, and are linked to a range of health and ecological risks. As regulatory scrutiny intensifies worldwide, so does the need for robust, sensitive, and comprehensive analytical methods to detect and quantify these elusive contaminants.

A recent LCGC International peer exchange, moderated by Rainer Lohmann, professor of oceanography, marine, and atmospheric chemistry at the University of Rhode Island, brought together leading scientists to discuss the analytical challenges of PFAS. The panel included Natalia Soares Quinete, assistant professor of chemistry and biochemistry at Florida International University, Stefan van Leeuwen senior scientist at Wageningen Food Safety Research, Wageningen University & Research, and Carrie McDonough assistant professor of chemistry at Carnegie Mellon University. Each brought unique perspectives on PFAS analysis—from environmental fate and remediation to food safety and untargeted screening techniques.

Here are the key takeaways from their discussion, with a focus on the technical hurdles, innovations, and emerging directions in PFAS analytics.

Mass Spectrometry: The Backbone of PFAS Analysis

At the heart of PFAS detection is mass spectrometry (MS), a cornerstone of analytical chemistry that offers both targeted and non-targeted capabilities. Quinete emphasized the utility of both low-resolution and high-resolution mass spectrometry in her work. Based at Florida International University, she focuses on PFAS fate, distribution, and remediation.

“I have been working a lot with mass spectrometry—both low- and high-resolution approaches,” she said. High-resolution mass spectrometry (HRMS), particularly time-of-flight (TOF) and orbital ion trap systems, enable the detection of hundreds of PFAS compounds in complex matrices.

Targeted MS remains the gold standard for regulatory monitoring, especially for well-characterized PFAS such as perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS). But high-resolution mass spectrometry (HRMS) has proven indispensable in identifying novel or ultra-short-chain PFAS—especially those not available as commercial standards. Quinete’s approach balances both: using targeted methods to quantify known compounds and untargeted workflows to uncover emerging or transformation products.

From the Environment to the Food Chain

Van Leeuwen provided a different but complementary angle. “My focus is on the food safety perspective and where that intersects with the environment,” he said. PFAS in water and soil inevitably find their way into the food chain—via fish, crops, and packaging materials.

Van Leeuwen’s group employs a hybrid strategy, combining targeted liquid chromatography (LC)–MS/MS methods with broader techniques like extractable organic fluorine (EOF) analysis. The EOF approach, while not compound-specific, captures the total fluorine content attributable to organofluorine compounds. It is particularly valuable when evaluating complex samples where traditional targeted PFAS panels might only scratch the surface.

He also emphasized the need for methods that are both sensitive and comprehensive, especially when translating analytical findings into exposure assessments and risk evaluations.

“We try to understand human exposure using the full analytical toolbox,” he said. “And that includes not just the known compounds, but the unknowns as well.”

Untargeted Analysis: Navigating the PFAS Unknowns

McDonough focuses on environmental chemistry and emerging contaminants. Her work leverages untargeted mass spectrometry to explore the vast chemical landscape of PFAS.

“Untargeted analysis is challenging,” McDonough said. “Because PFAS don’t always ionize consistently, and there’s a lack of reference standards.”

Yet, this strategy is vital for discovery science. Thousands of PFAS-related compounds exist across industrial and consumer applications, and new chemistries emerge regularly as manufacturers pivot in response to regulation.

McDonough highlighted that even untargeted workflows need to be grounded in chemical logic, using tools like fluorine-specific filters, suspect screening lists, and fragmentation pattern analysis to make sense of the data. For example, her team often combines LC–HRMS with software platforms like Compound Discoverer or XCMS to extract meaningful signals.

Moreover, she stressed the importance of data transparency and sharing, especially when dealing with unknowns. Repositories of spectra, suspect lists, and environmental samples are critical to building communal knowledge about PFAS occurrence and transformation.

Challenges Across the Analytical Workflow

The panelists agreed that the technical difficulties of PFAS analysis go beyond instrumentation. Here are several key challenges that analytical chemists continue to face:

Sample Preparation: PFAS are prone to ubiquitous contamination—from labware, solvents, and even air. Solid-phase extraction (SPE) is often used to isolate PFAS from matrices, but this step introduces potential biases. Recovery rates can vary significantly between short-chain and long-chain PFAS, necessitating meticulous method validation.

Matrix Effects: Environmental and biological samples present complex matrices—blood, soil, sediments, wastewater, and food—each with their own interferences. Ion suppression and enhancement during electrospray ionization (ESI) can skew quantitation. Matrix-matched calibration and isotopically labeled internal standards are critical for accurate results.

Lack of Analytical Standards: There are more than 10,000 known PFAS, yet only a few hundred are commercially available as reference standards. This limits the scope of both targeted analysis and method development. The analytical community continues to push for broader standard libraries and more open-access suspect lists.

Regulatory Dynamics: PFAS regulations are in flux. Different regions prioritize different compounds, and analytical methods must be adaptable. For instance, the European Union recently proposed a near-total ban on PFAS, while U.S. EPA’s current focus is on a few dozen high-risk compounds. Analytical labs must balance regulatory compliance with scientific exploration.

The Future of PFAS Analysis

When asked about future directions, all panelists underscored the need for method harmonization, international collaboration, and standardization efforts. As research pivots from legacy PFAS to emerging substitutes (like GenX or ADONA), laboratories must continuously evolve.

Innovations in fluorine-specific detection (like combustion ion chromatography for total fluorine), automated data processing, and machine learning-assisted spectral analysis may soon become routine in high-throughput PFAS labs.

Education and outreach are also essential. “We need to bring more early-career scientists into PFAS research,” Lohmann said. The complexity and relevance of PFAS chemistry offer rich ground for graduate students and postdocs seeking impactful research areas.

PFAS present one of the most analytically demanding and societally relevant challenges in environmental chemistry today. From trace-level quantitation in drinking water to tracking unknowns in the food chain, analytical chemists are on the front lines.

The panel discussion underscored that no single method or discipline can address the full PFAS puzzle. Instead, a combination of robust analytical techniques, interdisciplinary collaboration, and constant innovation will be required to understand—and ultimately mitigate—the risks posed by these persistent chemicals.

Watch the full panel discussion here.