Streamlined PFAS Annotation and Visualization with FluoroMatch Flow and Visualizer

Importance of the Topic

Per- and polyfluoroalkyl substances (PFAS) in food contact materials pose significant environmental and health risks due to their persistence and bioaccumulation potential.

Food packaging materials often contain greases and coatings that may leach unknown PFAS, creating a need for non-targeted screening methods to identify and quantify these compounds.

Objectives and Study Overview

This study presents FluoroMatch Flow and FluoroMatch Visualizer, an open-source workflow and interactive tool designed to automate the annotation, scoring, and visualization of PFAS compounds from high-resolution LC MS data.

The goals include improving annotation confidence, enabling homologous series exploration, and providing a freely available solution for the analytical community.

Methodology and Data Processing

Extraction and Analysis
Sample extracts from 23 food contact materials were prepared using EPA 1633 diluent with repeated vortexing, sonication, and storage steps. Analysis was performed on an ultra-high-performance liquid chromatography system coupled to an Agilent 6545 quadrupole time-of-flight mass spectrometer in negative electrospray mode over m/z 100–1100 with MS/MS at 0, 25, and 40 eV collision energy.

Data Processing Workflow
FluoroMatch Flow streamlines data conversion with msConvert, untargeted peak picking via MZmine 2.26, blank feature filtering, and PFAS annotation based on accurate mass, retention time, and in-silico fragmentation rules. Confidence levels are assigned using a rule-based scheme derived from the Schymanski scale.

Used Instrumentation

• Ultra-high-performance liquid chromatography (Agilent 1290 Infinity II)
• Quadrupole time-of-flight mass spectrometer (Agilent 6545 Q-TOF)
• Data processing software: msConvert, MZmine 2.26
• Visualization platform: Microsoft Power BI Desktop

Main Results and Discussion

In-silico Library Coverage
An in-silico fragmentation library of over 7000 PFAS across 72 subclasses was developed, achieving approximately 71% coverage of CF2-containing PFAS and an estimated 56% coverage based on normalized mass defect analysis.

Interactive Visualization
FluoroMatch Visualizer enables cross-filtered visualizations including mass defect plots, retention time correlations, MS/MS spectra overlays, and feature tables. Users can select homologous series for rapid trend identification and outlier detection.

Annotation Confidence
A systematic scoring framework communicates confidence for each feature, helping prioritize high-quality annotations and reduce false positives in complex nontargeted datasets.

Benefits and Practical Applications

• Automates labor-intensive steps in PFAS screening workflows
• Provides transparent confidence metrics to support regulatory reporting and research
• Enables detailed exploration of homologous series for source identification and pattern observation
• Open-source availability encourages community adoption and method standardization

Future Trends and Potential Applications

Expansion of In-silico Libraries and Machine Learning
Future development may focus on integrating machine learning to predict fragmentation patterns and extending libraries to include emerging PFAS and other halogenated compounds.

Cloud Deployment and Collaborative Platforms
Deploying FluoroMatch tools on cloud-based platforms could facilitate large-scale data sharing and collaborative research across laboratories and regulatory agencies.

Conclusion

FluoroMatch Flow and Visualizer deliver an open-source, rule-based framework for comprehensive PFAS annotation and interactive data exploration. By combining automated processing with intuitive visualization, this suite addresses critical challenges in nontargeted screening of PFAS in food contact materials.

References

1. U.S. Environmental Protection Agency. Comptox Chemicals Dashboard Master List of PFAS Substances Version 2. Accessed March 11 2021
2. Koelmel JP et al Toward Comprehensive Per- and Polyfluoroalkyl Substances Annotation Using FluoroMatch Software and Intelligent High-Resolution Tandem Mass Spectrometry Acquisition Analytical Chemistry 2020 92(16) 11186-11194
3. Koelmel JP et al Interactive Software for Visualization of Non-Targeted Mass Spectrometry Data FluoroMatch Visualizer ChemRxiv 2022
4. Coggan TL et al Single Analytical Method for the Determination of 50 Legacy and Emerging Per- and Polyfluoroalkyl Substances in Aqueous Matrices Analytical and Bioanalytical Chemistry 2019 411 3507-3520