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

Sousa, Pedro F. M.; Martella, Giulia; Åberg, K. Magnus; Esfahani, Bahare Kourangi; Motwani, Hitesh V.

doi:10.3390/toxics9040078

Cited by 22 publications

(39 citation statements)

References 25 publications

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“…Early DNA adductomics primarily utilized triple quadrupole instrumentation to perform neutral loss screening, 30 whereas more recent studies have taken advantage of HRMS, 4 which allows performing different types of acquisition modes such as DDAtriggered neutral loss, 9 wide selected ion monitoring tandem mass spectrometry (Wide-SIM/MS2), 10 and data independent acquisition (DIA). 6 Whereas DDA selects specific precursor ions for fragmentation resulting in clean MS2 spectra, DIA (or MS E ) fragments the entire range of ions, requiring elaborate data analysis software for the investigation of the spectra, 6 and a supplementary MS2 targeted acquisition for confirming the identity of the compound. However, the selective approach of DDA carries the risk of losing the fragmentation of the least abundant compounds.…”

Section: Acquisition Mode and Identification Approachmentioning

confidence: 99%

“…Whereas traditional -omics sciences rely on extensive existing database and software support, DNA adductomics is in a developmental phase. 5,6 A few studies have been published with the aim of building DNA adduct databases, which can be used as a tool for DNA adduct profiling. [7][8][9] A few other studies reported the development of untargeted DNA adductomics methods for identification of unknowns.…”

Section: ■ Introductionmentioning

confidence: 99%

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Development of an untargeted DNA adductomics method by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry

Barbera

Dragsted

2022

Preprint

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Cancer may be initiated by covalent modification of DNA by genotoxic molecules coming from diet, environment, inflammation, and other sources. For most of these genotoxicants there is little evidence of their identity. DNA adductomics is a new research field, aiming to screen for unknown DNA adducts by high resolution mass spectrometry (HRMS). However, due to the low abundance of DNA adducts, DNA adductomics presents several analytical challenges. In this work, a sensitive untargeted DNA adductomics method was developed by using ultra-high performance liquid chromatography (UHPLC) coupled via an electrospray ionization source (ESI) to a quadrupole-time of flight MS instrumentation. Mobile phases with ammonium bicarbonate gave the best signal enhancement. The MS capillary voltage, cone voltage and detector voltage had most effect on the response of the DNA adducts. A low adsorption vial was selected for reducing analyte loss. A hybrid surface coated HSST3 premier column was tested for reducing adsorption of the DNA adducts. The optimized method was applied to analyse DNA adducts in calf thymus and cat colon DNA by performing a MSE acquisition and screening for loss of deoxyribose, both in-source and in the fragmentation spectra, and for the nucleobase fragment ions. The putative DNA adducts were matched with an in-house DNA adduct database. Thirteen DNA adducts were observed in DNA from calf thymus and cat colon, four of them never reported before, showing promise for the application of this untargeted method in future human studies.

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Section: Acquisition Mode and Identification Approachmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Development of an untargeted DNA adductomics method by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry

Barbera

Dragsted

2022

Preprint

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“…DNA adductomics has been applied in studies of cancer − and ecotoxicology . For the detection of unknown DNA adducts, a method based on the neutral loss of 2′-deoxyribose from digested DNA samples has been used. , Recently, algorithms for the detection of such adducts in liquid chromatography–mass spectrometry (LC-MS) analysis have been created. , For protein adducts, adductomic approaches have been developed for serum albumin and hemoglobin (Hb) . Rappaport and collaborators have developed a method for the analysis of Cys34 adducts in serum albumin as 21-mer peptides after tryptic digestion .…”

Section: Introductionmentioning

confidence: 99%

Pathways to Identify Electrophiles In Vivo Using Hemoglobin Adducts: Hydroxypropanoic Acid Valine Adduct and Its Possible Precursors

Vryonidis

Karlsson

Aasa

et al. 2022

Chem. Res. Toxicol.

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Analytical methods and tools for the characterization of the human exposome by untargeted mass spectrometry approaches are advancing rapidly. Adductomics methods have been developed for untargeted screening of short-lived electrophiles, in the form of adducts to proteins or DNA, in vivo. The identification of an adduct and its precursor electrophile in the blood is more complex than that of stable chemicals. The present work aims to illustrate procedures for the identification of an adduct to N-terminal valine in hemoglobin detected with adductomics, and pathways for the tracing of its precursor and possible exposure sources. Identification of the adduct proceeded via preparation and characterization of standards of adduct analytes. Possible precursor(s) and exposure sources were investigated by measurements in blood of adduct formation by precursors in vitro and adduct levels in vivo. The adduct was identified as hydroxypropanoic acid valine (HPA-Val) by verification with a synthesized reference. The HPA-Val was measured together with other adducts (from acrylamide, glycidamide, glycidol, and acrylic acid) in human blood (n = 51, schoolchildren). The HPA-Val levels ranged between 6 and 76 pmol/g hemoglobin. The analysis of reference samples from humans and rodents showed that the HPA-Val adduct was observed in all studied samples. No correlation of the HPA-Val level with the other studied adducts was observed in humans, nor was an increase in tobacco smokers observed. A small increase was observed in rodents exposed to glycidol. The formation of the HPA-Val adduct upon incubation of blood with glycidic acid (an epoxide) was shown. The relatively high adduct levels observed in vivo in relation to the measured reactivity of the epoxide, and the fact that the epoxide is not described as naturally occurring, suggest that glycidic acid is not the only precursor of the HPA-Val adduct identified in vivo. Another endogenous electrophile is suspected to contribute to the in vivo HPA-Val adduct level.

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“…HPLC/ESI-MS/MS methodologies have significantly broadened the range of applications related to modified amino acids in general. The possibility to determine and characterize amino acid adducts to trace exposure to reactive electrophilic chemicals across the general population, such as from dietary intake or workplace environments, has paved the way for adductomics [24][25][26][27]. A highly selective MS platform that combines high-resolution, high m/z accuracy and ion fragmentation (tandem HRMS) would increase the possibility to identify and measure such trace levels of adducts, as has been reported in studies with DNA adducts [28][29][30].…”

Section: Introductionmentioning

confidence: 99%

Detection of Benzo[a]pyrene Diol Epoxide Adducts to Histidine and Lysine in Serum Albumin In Vivo by High-Resolution-Tandem Mass Spectrometry

Zurita

Motwani

Ilag

et al. 2022

Toxics

Self Cite

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Electrophilic diol epoxide metabolites are involved in the carcinogenicity of benzo[a]pyrene, one of the widely studied polycyclic aromatic hydrocarbons (PAHs). The exposure of humans to this PAH can be assessed by measuring stable blood protein adducts, such as to histidine and lysine in serum albumin, from their reactive metabolites. In this respect, measurement of the adducts originating from the genotoxic (+)-anti-benzo[a]pyrene diol epoxide is of interest. However, these are difficult to measure at such low levels as are expected in humans generally exposed to benzo[a]pyrene from air pollution and the diet. The analytical methods detecting PAH-biomarkers still suffer from low selectivity and/or detectability to enable generation of data for calculation of in vivo doses of specific stereoisomers, for evaluation of risk factors and assessing risk from exposures to PAH. Here, we suggest an analytical methodology based on high-pressure liquid chromatography (HPLC) coupled to high-resolution tandem mass spectrometry (MS) to lower the detection limits as well as to increase the selectivity with improvements in both chromatographic separation and mass determination. Method development was performed using serum albumin alkylated in vitro by benzo[a]pyrene diol epoxide isomers. The (+)-anti-benzo[a]pyrene diol epoxide adducts could be chromatographically resolved by using an HPLC column with a pentafluorophenyl stationary phase. Interferences were further diminished by the high mass accuracy and resolving power of Orbitrap MS. The achieved method detection limit for the (+)-anti-benzo[a]pyrene diol epoxide adduct to histidine was approximately 4 amol/mg serum albumin. This adduct as well as the adducts to histidine from (−)-anti- and (+/−)-syn-benzo[a]pyrene diol epoxide were quantified in the samples from benzo[a]pyrene-exposed mice. Corresponding adducts to lysine were also quantified. In human serum albumin, the anti-benzo[a]pyrene diol epoxide adducts to histidine were detected in only two out of twelve samples and at a level of approximately 0.1 fmol/mg.

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

Cited by 22 publications

References 25 publications

Development of an untargeted DNA adductomics method by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry

Development of an untargeted DNA adductomics method by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry

Pathways to Identify Electrophiles In Vivo Using Hemoglobin Adducts: Hydroxypropanoic Acid Valine Adduct and Its Possible Precursors

Detection of Benzo[a]pyrene Diol Epoxide Adducts to Histidine and Lysine in Serum Albumin In Vivo by High-Resolution-Tandem Mass Spectrometry

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