MeRgeION: a multifunctional R pipeline for small molecule LC-MS/MS data processing, searching, and organizing

Author(s): Youzhong Liu

Affiliation(s): de Duve Institute, UCLouvain



Small molecule structure elucidation using tandem mass spectrometry (MS/MS) plays a crucial role in life science, bioanalytical and pharmaceutical research. There is a pressing need for increased throughput of compound identification and transformation of historical data into information-rich spectral databases. Meanwhile, molecular networking, a recent bioinformatic framework, provides global displays and system-level understanding of complex LC-MS/MS datasets. Herein we present meRgeION, a multifunctional, modular, and flexible R-based toolbox to streamline spectral database building, automated structural elucidation, and molecular networking. The toolbox offers diverse tuning parameters and the possibility to combine various algorithms in the same pipeline. As an open-source R package, meRgeION is ideally suited for building spectral databases and molecular networks from privacy-sensitive and preliminary data. Using meRgeION, we have created an integrated spectral database covering diverse pharmaceutical compounds which was successfully applied to annotate drug-related metabolites from a published non-targeted metabolomics dataset as well as reveal the chemical space behind this complex dataset through molecular networking. Moreover, the meRgeION-based processing workflow has demonstrated the usefulness of spectral library search and molecular networking for pharmaceutical forced degradation studies. meRgeION is freely available at: https://github.com/daniellyz/meRgeION2.