FluoroMatch Flow: An Open Source HRMS PFAS Annotation Tool

Emerging Environmental Applications for High Resolution Mass Spectrometry
Oral Presentation

Prepared by S. Baumann1, J. Koelmel2, K. Hunt3, R. Hindle3
1 - Agilent, 3750 Brookside Pkwy., Suite 100, Alpharetta, GA, 30022, United States
2 - Yale School of Public Health, 60 College Street, New Haven, CT, 06510, United States
3 - Vogon Laboratory Svc Ltd, 34 Griffin Industrial Point, Unit 4, Cochrane, Alberta, AB T4C 0A3, Canada

Contact Information: [email protected]; 14084060484


Suspect and nontarget screening with liquid chromatography based high-resolution tandem mass spectrometry can be used for comprehensive characterization of PFAS. Many structure elucidation algorithms are focused on the six main chemical elements that are necessary for life, namely carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P) and sulfur (S). This means that they tend to perform poorly when confronted with anthropogenic compounds such as PFAS. To date, no automated open source PFAS data analysis software exists to mine fluorine-containing organic compounds. We introduced FluoroMatch, which automates file conversion, chromatographic peak picking, blank feature filtering, PFAS annotation based on precursor and fragment masses, and annotation ranking. The software library contains ∼7,000 PFAS fragmentation patterns based on rules derived from standards and literature, and the software automates a process to add additional compounds.

FluoroMatch Flow automates nontargeted and suspect screening workflow using multiple lines of evidence. FluoroMatch Flow directly processes vendor files and includes a systematic scoring framework to communicate confidence for every single feature, alongside also reporting confidence levels via the Schymanski schema. The integrated steps include file conversion using msConvert, a unique untargeted chromatographic peak picking strategy implementing MZmine, and blank feature filtering (BFF). It outputs annotations using exact mass and fragment masses, rankings of multiple annotations for features, and compilations of meta-data on fragmentation information and peaks used to annotate features.

To aid interpretation, we have added a Visualizer tool to the FluoroMatch suite of software based on Microsoft PowerBI. It provides interactive mass defect plots, accurate mass vs. retention time plots, MS/MS fragmentation plots, and annotation tables. Selecting a feature in one graph will adjust what is displayed in other views. This interactive cross-filtering allows simplified evaluation of a feature, PFAS series, or other groups of features. FluoroMatch Visualizer allows the investigation of trends across PFAS by narrowing down the number of features. One of the most useful approaches is to select individual homologous series, automatically determined using nominal mass and normalized mass defect. When series are selected, all visuals, including MS/MS spectra, are updated to show all members of a series overlaid. Then patterns can easily be observed, and outliers determined. Tens to hundreds of series often exist, and therefore series can further be narrowed down easily by those containing high scores or certain characteristic PFAS fragments.