Mass Spectral Library for DNA Adductomics

Abstract

Endogenous electrophiles, ionizing and non-ionizing radiation, and hazardous chemicals present in the environment and diet can damage DNA by forming covalent adducts. DNA adducts can form in critical cancer driver genes and, if not repaired, may induce mutations during cell division, potentially leading to the onset of cancer. The detection and quantification of specific DNA adducts are some of the first steps in studying their role in carcinogenesis, the physiological conditions that lead to their production, and the risk assessment of exposure to specific genotoxic chemicals. Hundreds of different DNA adducts have been reported in the literature, and there is a critical need to establish a DNA adduct mass spectral database to facilitate the detection of previously observed DNA adducts and characterize newly discovered DNA adducts. We have collected synthetic DNA adduct standards from the research community, acquired MSⁿ (n = 2, 3) fragmentation spectra using Orbitrap and Quadrupole-Time-of-Flight (Q-TOF) MS instrumentation, processed the spectral data and incorporated it into the MassBank of North America (MoNA) database, and created a DNA adduct portal Web site (https://sites.google.com/umn.edu/dnaadductportal) to serve as a central location for the DNA adduct mass spectra and metadata, including the spectral database downloadable in different formats. This spectral library should prove to be a valuable resource for the DNA adductomics community, accelerating research and improving our understanding of the role of DNA adducts in disease.

Figure 1.. Comparison of Orbitrap HCD, Orbitrap CID and Q-TOF MS² spectra.

The Orbitrap HCD collision energies are typically reported in units of percentages to relate the CID and HCD collision energies to each other for Thermo Scientific Orbitrap instrumentation. The collision energies in electron-volt (eV) units are listed in parentheses for the HCD MS² spectra for comparison with the Q-TOF MS² spectra.

Figure 2.. Comparison of product ion spectra under different formation mechanisms.

(A) MS² spectrum of the protonated 1,N⁶-benzoquinone-adenine ion using the synthetic standard. (B) MS² spectrum of protonated 1,N⁶-benzoquinone-adenine ion produced upon in-source fragmentation of the protonated 1,N⁶-benzoquinone-deoxyadenosine ion. (C) Spectrum of protonated 1,N⁶-benzoquinone-adenine ion (MS³) produced upon MS² fragmentation of the protonated 1,N⁶-benzoquinone-deoxyadenosine ion.

Figure 3.

(A) Library formats, (B) Library usages

Figure 4.. Representative search of spectra from the LC-MS³ Orbitrap analysis of hydrolyzed DNA from human bladder cancer cells against the DNA adduct database using the NIST MS Search algorithm with manual review.

(Top spectrum, red) DNA sample from human bladder cancer cells (Bottom spectrum, blue) 8-(4-ABP)-dG library entry.