MeRgeION: a Multifunctional R Pipeline for Small Molecule LC-MS/MS Data Processing, Searching, and Organizing

Area of Science:

• Analytical Chemistry
• Bioinformatics
• Computational Chemistry

Background:

• Tandem mass spectrometry (MS/MS) is vital for small molecule structure elucidation in life sciences and pharmaceuticals.
• High-throughput compound identification and data transformation into spectral databases are critical research needs.
• Molecular networking offers a powerful framework for analyzing complex LC-MS/MS data and understanding chemical space.

Purpose of the Study:

• To introduce meRgeION, a versatile R-based toolbox designed to streamline spectral database construction, automated structural elucidation, and molecular networking.
• To provide a flexible platform for integrating diverse algorithms and tuning parameters for advanced data analysis.
• To facilitate the creation of spectral databases and molecular networks from sensitive and preliminary data.

Main Methods:

• Development of meRgeION, an open-source R package with modular functionalities.
• Creation of an integrated spectral database for diverse pharmaceutical compounds.
• Application of meRgeION for annotating drug metabolites and exploring chemical space in metabolomics data.
• Utilizing meRgeION for pharmaceutical forced degradation studies via spectral library search and molecular networking.

Main Results:

• Successfully created an integrated spectral database of pharmaceutical compounds.
• Demonstrated effective annotation of drug-related metabolites from nontargeted metabolomics data.
• Revealed the underlying chemical space of complex datasets using molecular networking.
• Validated the utility of meRgeION in pharmaceutical forced degradation studies.

Conclusions:

• meRgeION is a powerful, flexible, and open-source tool for enhancing spectral database building, automated structural elucidation, and molecular networking.
• The toolbox significantly aids in the analysis of complex LC-MS/MS data, accelerating compound identification and data interpretation.
• meRgeION is valuable for various research applications, including metabolomics and pharmaceutical stability studies.