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PFAS analysis is complex, but expert guidance doesn’t have to be. In this episode of our ‘Ask the PFAS expert series’, we’re joined by Michael Scherer, Application Lead for Food and Environmental, to answer the most pressing questions in PFAS analysis. From why LC-MS/MS systems are the gold standard for analyzing diverse PFAS compounds, to which EU methods deliver reliable results for drinking water, and to practical steps to prevent contamination, Michael shares actionable insights to help laboratories achieve accuracy, consistency, and confidence in their workflows.

1. What is the primary advantage of using LC-MS/MS systems for PFAS analysis?

LC-MS/MS systems offer a major advantage for PFAS analysis by enabling the detection of a wide range of compounds in a single, comprehensive method. PFAS includes multiple classes—such as carboxylic acids, sulfonic acids, and newer compounds like GenX—each with different chain lengths and polarities. LC-MS/MS handles this complexity efficiently. Modern platforms with fast polarity switching can even include compounds such as Capstone A and B, further expanding coverage. Since these methods typically rely on reversed-phase chromatography, they deliver high reliability and reproducibility, ensuring consistent results over time.

2. Which standardized method is compatible with SCIEX LC-MS/MS systems for analyzing PFAS in drinking water?

The European Union Method 17892 is the standard for PFAS analysis in drinking water. It uses a direct injection technique, typically with a 100 µL sample injection volume, making it straightforward and efficient. This method is highly compatible with SCIEX LC-MS/MS systems, particularly the QTRAP 6500+ system, and the SCIEX 7500+ system, and delivers excellent performance and reliability across these platforms.

3. What are the best practices to avoid PFAS contamination?

To minimize PFAS contamination, start with your equipment. Installing a PFAS kit on your LC system is one of the most effective steps. This involves replacing any components that may contain PFAS with alternative materials, such as swapping fluoropolymer solvent tubing for PEEK or Polyethylene tubing. This simple change can significantly reduce interference and stabilise concentrations. Another key change is using a delay column, which helps separate the system delay peak from the analytical peak for more accurate results. Finally, always choose the highest-grade solvents and reagents available—water, methanol, acetonitrile, formic acid, acetic acid, ammonium format, and more—and whenever possible, opt for PFAS-free materials. Many manufacturers now offer PFAS-tested products designed explicitly for PFAS analysis, so make these your standard choice for cleaner workflows.

What is the typical detection limit for PFAS using LC-MS MS systems?

So, when we talk about the SCIEX 7500+ system, which is our highest-end platform, we can reach super low limits today. When we talk about drinking water, we must always look at the regulations, which are different in different geographical regions. One of the lowest limits that we have is the so-called sum of four PFAS  (PFOS, PFOA, PFHxS, PFNA) which is two nanograms per liter in water. But with the dilution that we have, typically 50 / 50 with an organic part, then we need to be able to reach lower limits in the vial: 0.25 ng/L for each compound. And this is easily accessible with the SCIEX 7500+ system using a 100-microliter injection for water samples. When we talk about food, the EU-regulation 2022/1431 (August 2022) has recommended limits of 0.001 microgram per kilogram in plant-based foods. And we can also reach this with the SCIEX 7500+ system. So, it depends, of course, on the pre-concentration factor that you use during the sample preparation. But one recommendation here is to use a high-end platform for this kind of analysis. Because the lower your pre-concentration factor is, the fewer issues you have with blank concentrations, because you also enrich all matrix interferences, which are very hard to remove. It’s easier to use a high-end platform with less sample pre-concentration and small injection volumes. Through this approach you can get much more consistent results over time.

What is a common challenge when analyzing PFAS in water using LC-MS MS?

One of the typical issues is that we cover such a large range of polarity. For example, the carboxylic and sulfonic acids monitored in most methods have chain lengths that range between C4 and C13. They are quite different in polarity and solubility in water. This means the long chain length compounds can have issues with linearity because they are adsorbed to materials during the analysis, they disappear from the analysts view

To counter adsorption we need to add a certain part of organic solvent. And we typically use polypropylene vials instead of glass vials as the long chain PFAS bind less to polypropylene. The short chain-length PFAS, such as PFBA and PFPeA have issues when the sample gets loaded onto the column with large volume injections. For these injections it is helpful to add some acids into the vial and to work with columns which can have a high loading capability. At the end, we balance here the polarity and the solubility to have a good analytical results.

Have more questions? We’d love to hear them! Send your queries to our PFAS experts and we’ll feature them in future Q&A sessions.

A big thank you to Michael for sharing such valuable insights in this edition of our Ask the PFAS expert series.

You can also connect with Michael and our team on LinkedIn – we’re always happy to chat and help you optimise your workflows.

Stay tuned for the next instalment in the series!