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HDPairFinder: A data processing platform for hydrogen/deuterium isotopic labeling-based nontargeted analysis of trace-level amino-containing chemicals in environmental water


Tao Huan , Tingting Zhao , Kristin Carroll , Caley B. Craven , Nicholas J.P. Wawryk , Shipei Xing , Jian Guo , Xing-Fang Li

DOI:10.1016/j.jes.2023.02.033

Received December 30, 2022,Revised , Accepted February 16, 2023, Available online February 25, 2023

Volume 36,2024,Pages 583-593

The combination of hydrogen/deuterium (H/D) formaldehyde-based isotopic methyl labeling with solid-phase extraction and high-performance liquid chromatography–high resolution mass spectrometry (HPLC-HRMS) is a powerful analytical solution for nontargeted analysis of trace-level amino-containing chemicals in water samples. Given the huge amount of chemical information generated in HPLC-HRMS analysis, identifying all possible H/D-labeled amino chemicals presents a significant challenge in data processing. To address this, we designed a streamlined data processing pipeline that can automatically extract H/D-labeled amino chemicals from the raw HPLC-HRMS data with high accuracy and efficiency. First, we developed a cross-correlation algorithm to correct the retention time shift resulting from deuterium isotopic effects, which enables reliable pairing of H- and D-labeled peaks. Second, we implemented several bioinformatic solutions to remove false chemical features generated by in-source fragmentation, salt adduction, and natural 13C isotopes. Third, we used a data mining strategy to construct the AMINES library that consists of over 38,000 structure-disjointed primary and secondary amines to facilitate putative compound annotation. Finally, we integrated these modules into a freely available R program, HDPairFinder.R. The rationale of each module was justified and its performance tested using experimental H/D-labeled chemical standards and authentic water samples. We further demonstrated the application of HDPairFinder to effectively extract N-containing contaminants, thus enabling the monitoring of changes of primary and secondary N-compounds in authentic water samples. HDPairFinder is a reliable bioinformatic tool for rapid processing of H/D isotopic methyl labeling-based nontargeted analysis of water samples, and will facilitate a better understanding of N-containing chemical compounds in water.

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