SETAC: FluoroMatch Flow and Visualizer are New Tools for Streamlined PFAS Annotation and Visualization

Importance of the Topic

Persistent per- and polyfluoroalkyl substances represent a growing environmental and health concern due to their resistance to degradation and widespread occurrence. Reliable detection and structural annotation of PFAS in complex samples are essential for monitoring contamination, guiding remediation efforts, and informing regulatory policies. The development of specialized open source tools addresses critical gaps in existing non-targeted screening workflows that often struggle with fluorinated chemistries.

Objectives and Study Overview

This work presents FluoroMatch Flow and FluoroMatch Visualizer, two integrated tools designed to streamline suspect and non-target PFAS analysis based on liquid chromatography high-resolution tandem mass spectrometry data. The objectives are to automate data conversion, peak detection, blank feature removal, annotation scoring, and interactive visualization, thereby increasing throughput and confidence in PFAS identification.

Methodology and Instrumentation

Sample preparation involved a 1:100,000 dilution of an aqueous film forming foam extract in 70:30 water methanol with four replicate injections. Analysis was performed on an Agilent 1290 Infinity II UHPLC coupled to a 6545 quadrupole time-of-flight mass spectrometer operating in negative electrospray mode. Data acquisition covered m/z 100–1100 with collision energies of 0, 25, and 40 eV. FluoroMatch Flow automates file conversion via msConvert, chromatographic peak picking using MZmine 3.0 or user algorithms, and blank feature filtering. A curated library of approximately 7,000 PFAS fragmentation patterns guides in-silico annotation and ranking according to the Schymanski confidence schema.

Main Results and Discussion

FluoroMatch Flow generated systematic annotations with confidence scores for every detected feature. Iterative data-dependent MS/MS acquisition doubled confident identifications and quadrupled tentative identifications, although exact mass evidence alone remained a limitation for one-third of features. Coverage estimation using all-ion fragmentation and normalized mass defect plots indicated 71 percent fragmentation coverage for CF2-containing PFAS and 56 percent overall when accounting for false negatives. FluoroMatch Visualizer, implemented in Power BI Desktop, offers interactive mass defect versus retention time plots, overlayed MS/MS spectra for homologous series, fragment screening tables, and customizable dashboards to prioritize high-confidence features.

Benefits and Practical Applications

• End-to-end automation reduces manual data processing and potential errors.
• Scoring framework improves transparency and comparability of annotations.
• Open source accessibility fosters community development and library expansion.
• Customizable visualizations accelerate interpretation of large non-target datasets.

Future Trends and Potential Uses

Expansion of in-silico fragmentation libraries guided by experimental mapping will enhance coverage of emerging PFAS. Integration with machine learning algorithms can improve prediction of novel compounds and reduce false positives. Cloud-based deployment and interoperability with other mass spectrometry platforms will facilitate large-scale environmental monitoring and cross-laboratory data sharing.

Conclusion

FluoroMatch Flow and Visualizer provide a comprehensive, configurable solution for PFAS annotation in non-targeted LC-HRMS workflows. By combining automated data processing, rule-based scoring, and interactive dashboards, these tools enhance confidence, reproducibility, and throughput in PFAS research and regulatory applications.

Reference

1. 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.
2. Schymanski EL et al. Identifying Small Molecules via High Resolution Mass Spectrometry Communicating Confidence. Environmental Science & Technology 2014, 48(4):2097-2098.
3. McDonough CA et al. Bioaccumulation of Novel Per- and Polyfluoroalkyl Substances in Mice Dosed with an Aqueous Film-Forming Foam. Environmental Science & Technology 2020, 54(9):5700-5709.
4. Koelmel JP et al. FluoroMatch 2.0 – making automated and comprehensive non-targeted PFAS annotation a reality. Analytical and Bioanalytical Chemistry 2022, 414:1201-1215.
5. Coggan TL et al. Single analytical method for the determination of 50 legacy and emerging PFAS in aqueous matrices. Analytical and Bioanalytical Chemistry 2019, 411:3507-3520.