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Abstract
Colorectal cancer (CRC) may develop after covalent modification of DNA by exogenous or endogenous genotoxic molecules coming from smoke, meat intake, inflammation or other factors. Several genotoxicants are known to cause DNA damage, but there is little evidence on their identity. DNA adductomics is a new research field, aiming to screen 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 electrospray ionization source (ESI) to quadrupole-time of flight MS (Vion-qTOF). Mobile phases with ammonium bicarbonate gave the best signal enhancement. The MS capillary voltage, the cone voltage and the detector voltage mainly affected the response of the DNA adducts. A low adsorption vial was selected for reducing analyte loss. A hybrid surface coated HSST3 premier column showed a minimal adsorption of the DNA adducts. The optimized method was applied to analyse DNA from calf thymus and cat colon by performing a MSE acquisition screening for the loss of -dR, both in source and in the fragmentation spectra, and for the nucleobase fragment ions, to select the potential DNA adducts. Thirteen DNA adducts were observed in DNA from calf thymus and cat colon, showing good promise for the application of this untargeted method in future human studies.
Supplementary materials
Title
Supplementary material
Description
List of the different tested chromatographic (Table S1) and mass spectrometric (Table S2); Settings for the pre-processing of the chromatographic runs with MZmine 2.53 (Table S3.1) and UNIFI 1.9.4.053 (Table S3.2); Results of the chromatographic optimization in terms of signal intensity with HCOOH (Figure S4.1), CH3COOH (Figure S4.2), CH3COONH4 (Figure S4.3), HCOONH4 (Figure S4.4), NH4HCO3 (Figure S4.5); Results of the chromatographic optimization in terms of peak asymmetry factor (Figure S4.6), peak capacity (Figure S4.7), retention time standard deviation (Figure S4.8), resolution (Table S4.1); comparison of glass vs polyethylene bottles (Figure S4.9); Results of mass spectrometric optimization (Figure S5.1); Results of adsorption processes in terms of comparison among different low adsorption vials (Figure S6.1), comparison between the columns Premier HSST3 and HSST3 (Figure S6.2); Results of the screening (Table S7.1) and the identification of the DNA adducts in real samples (Table S7.2) and relative structures (Figure S7.1).
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