Simultaneous RNA and DNA Adductomics Using Single Data-Independent Acquisition Mass Spectrometry Analysis

Area of Science:

• Environmental chemistry
• Molecular biology
• Analytical chemistry

Background:

• Adductomics studies analyze chemical modifications of nucleic acids and proteins.
• High-resolution tandem mass spectrometry (HRMS/MS) has advanced adductomics methods.
• Simultaneous analysis of RNA and DNA adducts is challenging but valuable.

Purpose of the Study:

• To develop and demonstrate a novel HRMS-based method for simultaneous RNA and DNA adduct analysis.
• To apply this method to Baltic amphipods as sentinels of environmental disturbances.
• To identify and characterize RNA adducts in these organisms.

Main Methods:

• Developed a single-injection HRMS method using Orbitrap HRMS with full scan and data-independent acquisition.
• Utilized the open-source program 'nLossFinder' for adduct identification based on characteristic neutral losses.
• Employed the MODOMICS database for structural identification of RNA adducts.

Main Results:

• Successfully detected approximately 60 putative RNA adducts in Baltic amphipods, in addition to known DNA adducts.
• Identified RNA adducts included methylation and deamination products (inosine).
• 54 RNA adducts remain structurally unidentified, indicating potential for new discoveries.

Conclusions:

• The developed multi-adductomics method enables simultaneous screening of RNA and DNA adducts.
• This approach identified novel RNA adducts in environmental sentinels.
• The methodology holds potential for developing biomarkers to diagnose pollution effects in biota.