Large-Scale Quantification of Xenobiotics Following Non-Targeted Liquid Chromatography Tandem Mass Spectrometry

The diversity of anthropogenic organic substances in aquatic environments creates a need for analytical workflows that combine chemical coverage with reliable quantification, in order to assess global chemical pollution. Here, we present an integrated workflow that combines non-targeted and targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) for the analysis of xenobiotics in river and coastal environments. We developed a web-based application, GNPS2-Quant, to convert data-dependent acquisition (DDA) results into scheduled inclusion lists for parallel reaction monitoring (PRM), using precursor m/z values and retention times, thereby accelerating the transfer from non-targeted discovery to targeted quantification within the same instrument platform. Using a quadrupole orbitrap (Exploris 480) instrument and a panel of 142 xenobiotics, we compared the quantification performance of full-scan DDA-MS1 data vs PRM. While PRM provides greater selectivity, DDA-MS1 generally provided greater sensitivity, yielding lower limits of detection for 61 compounds and lower limits of quantification for 61 compounds. Despite these differences, both methods showed comparable quantitative accuracy, with approximately 75% of quality control measurements meeting our precision criteria, which was in a similar range to measurements using multiple reaction monitoring (MRM) on a triple quadrupole mass spectrometer. Application to Southern California river and estuary samples enabled the quantification of 57 xenobiotics, with strong agreement between methods across sites. While our results highlight the utility of PRM generation from non-targeted LC-MS/MS data, our data also demonstrate that DDA-MS1 alone can provide scalable quantitative performance, avoiding costly and time-consuming reanalysis.