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Related Experiment Video

Updated: Jul 15, 2025

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow

Published on: April 18, 2019

Expanding Per- and Polyfluoroalkyl Substances Coverage in Nontargeted Analysis Using Data-Independent Analysis and

Jeremy P Koelmel¹, Michael Kummer², Olivier Chevallier³

¹Department of Environmental Health Science, Yale School of Public Health, New Haven, Connecticut 06520, United States.

Journal of the American Society for Mass Spectrometry

|September 26, 2023

Summary

IonDecon software improves per- and polyfluoroalkyl substances (PFAS) analysis by filtering All Ions data. This enhances PFAS identification in complex environmental samples, aiding regulatory development.

Keywords:

All Ions fragmentation DDA DIA PFAS domestic sewage high-resolution mass spectrometry

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Area of Science:

Environmental Chemistry
Analytical Chemistry
Mass Spectrometry

Background:

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants with known health risks.
Current PFAS analysis using UHPLC HRMS/MS with data-dependent acquisition (DDA) has limitations in ion selection.
All Ions fragmentation (AIF) offers broader ion coverage but suffers from high false positive rates due to lost precursor-fragment relationships.

Purpose of the Study:

To introduce IonDecon software for filtering AIF data to improve PFAS identification.
To assess the accuracy and effectiveness of IonDecon in deconvoluting AIF files for nontargeted PFAS analysis.
To evaluate the impact of IonDecon on PFAS MS/MS coverage in complex environmental samples.

Main Methods:

Development and application of IonDecon software to filter All Ions fragmentation data.
Comparison of PFAS annotation accuracy between IonDecon with AIF and traditional DDA in neat solutions.
Evaluation of IonDecon's impact on PFAS MS/MS coverage in complex matrices like domestic sewage.

Main Results:

IonDecon successfully deconvolutes AIF data, generating open-source DDA-formatted files for downstream analysis.
In neat solutions, IonDecon with AIF achieved comparable false positive rates to DDA, accurately annotating PFAS standards.
AIF combined with IonDecon significantly enhanced PFAS MS/MS coverage in complex samples, tripling annotations in domestic sewage.
While IonDecon improved data quality, some false fragments persisted in complex samples, suggesting the continued utility of DDA.

Conclusions:

IonDecon is a valuable tool for deconvoluting AIF data, improving PFAS identification and coverage in environmental analysis.
Integrating AIF and IonDecon into analytical workflows can substantially increase the number of identifiable PFAS, including novel compounds.
While AIF and IonDecon enhance nontargeted analysis, combining them with DDA is recommended for minimizing false positives in complex samples.