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FluoroMatch 2.0—making automated and comprehensive non-targeted PFAS annotation a reality

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Abstract

Because of the pervasiveness, persistence, and toxicity of per- and polyfluoroalkyl substances (PFAS), there is growing concern over PFAS contamination, exposures, and health effects. The diversity of potential PFAS is astounding, with nearly 10,000 PFAS catalogued in databases to date (and growing). The ability to detect the thousands of known PFAS, and discover previously uncatalogued PFAS, is necessary to understand the scope of PFAS contamination and to identify appropriate remediation and regulatory solutions. Current non-targeted methods for PFAS analysis require manual curation and are time-consuming, prone to error, and not comprehensive. FluoroMatch Flow 2.0 is the first software to cover all steps of data processing for PFAS discovery in liquid chromatography–high-resolution tandem mass spectrometry samples. These steps include feature detection, feature blank filtering, exact mass matching to catalogued PFAS, mass defect filtering, homologous series detection, retention time pattern analysis, class-based MS/MS screening, fragment screening, and predicted MS/MS from SMILES structures. In addition, a comprehensive confidence level criterion is implemented to help users understand annotation certainty and integrate various layers of evidence to reduce overreporting. Applying the software to aqueous film forming foam analysis, we discovered over one thousand likely PFAS including previously unreported species. Furthermore, we were able to filter out 96% of features which were likely not PFAS. FluoroMatch Flow 2 increased coverage of likely PFAS by over tenfold compared to the previous release. This software will enable researchers to better characterize PFAS in the environment and in biological systems.

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Data availability

The final annotated excel sheets with feature intensities, annotations, homologous series groupings, etc., are available as a supplemental excel file with the online version of this manuscript. The raw Agilent “.d” files can be downloaded at: ftp://massive.ucsd.edu/MSV000086811/updates/2021-02-05_jeremykoelmel_e5b21166/raw/McDonough_AFFF_3M_ddMS2_Neg.zip

(Note use Google Chrome or Firefox, Microsoft Edge and certain other browsers are unable to download from an ftp link).

Code availability

The FluoroMatch Software platform and written and video tutorials are available at: http://innovativeomics.com/software/fluoromatch-flow-covers-entire-pfas-workflow/

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Acknowledgements

A large array of PFAS standards used to develop libraries were donated by SynQuest Labs, Inc. and Oakwood Products, Inc.

Funding

S.L.N was supported by USDA NIFA Hatch funds (CONH00789). JAB received support from the U.S. Environmental Protection Agency under the Science To Achieve Results (STAR) grant programs: EPA-G2018-STAR-B1—Grant#: 83962001-0—and EPA-G2019-STAR-E1—Grant#: 84004501-0. J.P.K and K.J.G.P. received support from Agilent Technologies ACT-UR grant mechanism.

Author information

Author notes

  1. Jeremy P. Koelmel and Paul Stelben contributed equally to this work.

Authors and Affiliations

  1. School of Public Health, Yale University, New Haven, CT, USA

    Jeremy P. Koelmel, Paul Stelben, Elizabeth Lin & Krystal J. Godri Pollitt

  2. Department of Civil Engineering, Stony Brook University, Stony Brook, NY, USA

    Carrie A. McDonough & David A. Dukes

  3. Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, FL, USA

    Juan J. Aristizabal-Henao & John A. Bowden

  4. Departments of Environmental Sciences and Analytical Chemistry, The Connecticut Agricultural Experiment Station, New Haven, CT, USA

    Sara L. Nason

  5. Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA

    Yang Li

  6. Innovative Omics Inc., Sarasota, FL, USA

    Sandi Sternberg

  7. Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3FL, UK

    Manfred Beckmann, John Draper & Jasen P. Finch

  8. Center for Computational Toxicology and Exposure, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, Durham, NC, 27711, USA

    Antony J. Williams

  9. Department of Clinical Biochemistry, Amager and Hvidovre Hospital, 2650, Hvidovre, Denmark

    Jens K. Munk

  10. SynQuest Laboratories, Alachua, FL, USA

    Chris Deigl

  11. Agilent Technologies Inc., Santa Clara, CA, USA

    Emma E Rennie

  12. Department of Chemistry, University of Florida, Gainesville, FL, USA

    John A. Bowden

Authors
  1. Jeremy P. Koelmel
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  2. Paul Stelben
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  3. Carrie A. McDonough
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  4. David A. Dukes
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  9. Elizabeth Lin
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  18. Krystal J. Godri Pollitt
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Contributions

JP Koelmel—Algorithm concepts, software development, writing manuscript, and data processing. P Stelben—Software development, writing manuscript, and data processing. CA McDonough—Data acquisition, data analysis, and writing manuscript. DA Dukes—Data acquisition, data analysis, and writing manuscript. JJ Aristizabal-Henao—Data acquisition and writing manuscript. SL Nason—Testing software and writing manuscript. Y Li—software development (interface). S Sternberg—Developing tutorial material. E Lin—sample handling and preparation. M Beckmann—Data processing and manuscript writeup. AJ Williams—Data processing and manuscript writeup. J Draper—Data processing and manuscript writeup. JP Finch—Data processing and manuscript writeup. JK Munk—software development. C Deigl—Funding and manuscript writeup. EE Rennie—Funding, data processing, and manuscript writeup. JA Bowden—Algorithm concepts, funding, and manuscript writeup. KJG Pollitt—Funding and manuscript writeup.

Corresponding authors

Correspondence to John A. Bowden or Krystal J. Godri Pollitt.

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Published in the topical collection Per- and Polyfluoroalkyl Substances (PFAS) – Contaminants of Emerging Concern with guest editors Erin Baker and Detlef Knappe.

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Koelmel, J.P., Stelben, P., McDonough, C.A. et al. FluoroMatch 2.0—making automated and comprehensive non-targeted PFAS annotation a reality. Anal Bioanal Chem 414, 1201–1215 (2022). https://doi.org/10.1007/s00216-021-03392-7

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