NLossFinder-A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts.

Pedro Sousa,Giulia Martella,Hitesh Motwani,Bahare Esfahani,K Åberg

doi:10.3390/toxics9040078

Abstract

DNA adductomics is a relatively new omics approach aiming to measure known and unknown DNA modifications, called DNA adducts. Liquid chromatography–tandem mass spectrometry (LC-MS/MS) has become the most common method for analyzing DNA adducts. Recent advances in the field of mass spectrometry have allowed the possibility to perform a comprehensive analysis of adducts, for instance, by using a nontargeted data-independent acquisition method, with multiple precursor m/z windows as an inclusion list. However, the generated data are large and complex, and there is a need to develop algorithms to simplify and automate the time-consuming manual analysis that has hitherto been used. Here, a graphical user interface (GUI) program was developed, with the purpose of tracking a characteristic neutral loss reaction from tandem mass spectrometry of the nucleoside adducts. This program, called nLossFinder, was developed in the MATLAB platform, available as open-source code. Calf thymus DNA was used as a model for method optimization, and the overall adductomics approach was applied to DNA from amphipods (Monoporeia affinis) collected within the Swedish National Marine Monitoring Program. In the amphipod DNA, over 150 putative adducts were found in comparison to 18 using a manual approach in a previous study. The developed program can improve the processing time for large MS data, as it processes each sample in a few seconds, and hence can be applicable for high-throughput screening of adducts.

Highlights

DNA adducts are modifications on the genome resulting from the covalent binding of structural moieties on the nucleosides, or the molecular rearrangement of the nucleosides, associated with exposure to xenobiotics and endogenous processes
A peak is detected when a part of the signal data in each pure-ion chromatograms (PICs) has a Gaussian shape, or alike, i.e., parts of the signal that have an increasing slope, followed by a decreasing slope, that can be distinguished from noise
A program with a graphical user interface (GUI) was developed for the detection of DNA adducts, which has a scope to advance the field of DNA adductomics

Summary

Introduction

DNA adducts are modifications on the genome resulting from the covalent binding of structural moieties on the nucleosides, or the molecular rearrangement of the nucleosides, associated with exposure to xenobiotics and endogenous processes. In our previous study [6], an HRMS-based adductomics approach was employed using M. affinis sampled within the scope of the Swedish National Marine Monitoring Program (SNMMP), conducted by the Swedish Environmental Protection Agency In this sample set, only 18 adducts were found by processing the DIA data manually. The developed program is based on finding a neutral loss difference between precursors (MS1) and adducted nucleobase fragments (MS2) with high mass accuracy The workflow of this approach for DNA adductomics is described along with the existing challenges. NLossFinder was developed to find neutral losses in DIA data by an untargeted approach; a feature extraction method was introduced in the program to reduce the complexity of the data This feature extraction method was adapted from TracMass2 [20] and consists of a two-step algorithm process. Detailed instructions on the prerequisites, installation and operation of the program are presented in the Supplementary Information

Experimental

Results and Discussion

Conclusions