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nLossFinder—A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts

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...

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Autores principales: Sousa, Pedro F. M., Martella, Giulia, Åberg, K. Magnus, Esfahani, Bahare, Motwani, Hitesh V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067598/
https://www.ncbi.nlm.nih.gov/pubmed/33916914
http://dx.doi.org/10.3390/toxics9040078
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author Sousa, Pedro F. M.
Martella, Giulia
Åberg, K. Magnus
Esfahani, Bahare
Motwani, Hitesh V.
author_facet Sousa, Pedro F. M.
Martella, Giulia
Åberg, K. Magnus
Esfahani, Bahare
Motwani, Hitesh V.
author_sort Sousa, Pedro F. M.
collection PubMed
description 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.
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spelling pubmed-80675982021-04-25 nLossFinder—A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts Sousa, Pedro F. M. Martella, Giulia Åberg, K. Magnus Esfahani, Bahare Motwani, Hitesh V. Toxics Article 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. MDPI 2021-04-07 /pmc/articles/PMC8067598/ /pubmed/33916914 http://dx.doi.org/10.3390/toxics9040078 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sousa, Pedro F. M.
Martella, Giulia
Åberg, K. Magnus
Esfahani, Bahare
Motwani, Hitesh V.
nLossFinder—A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts
title nLossFinder—A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts
title_full nLossFinder—A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts
title_fullStr nLossFinder—A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts
title_full_unstemmed nLossFinder—A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts
title_short nLossFinder—A Graphical User Interface Program for the Nontargeted Detection of DNA Adducts
title_sort nlossfinder—a graphical user interface program for the nontargeted detection of dna adducts
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8067598/
https://www.ncbi.nlm.nih.gov/pubmed/33916914
http://dx.doi.org/10.3390/toxics9040078
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