Multiple Spectrum Alignment for Molecular Networking Exploration and Discovery.

Molecular networking is a computational mass spectrometry technique used to visualize and connect tandem mass spectra from putatively related molecules to reveal structural relationships. Despite their utility, existing tools for interpreting molecular networks are limited in the ability to easily organize fragmentation patterns within molecular families. We developed an interactive web-based tool, the Multiple Mass Spectral Alignment (MMSA) approach, that enhances the visualization of molecular networks by displaying detailed spectral alignment information among all the spectra in a network component in one visualization. MMSA identifies sets of consensus peaks that contribute to the alignment of multiple tandem mass spectra, offering insights into how structural moieties captured by specific fragments influence the construction of molecular networks. We demonstrate that MMSA facilitates insightful understanding of molecular networks and improves the interpretability of the tandem mass spectra, capturing the chemical modifications or core structures within a molecular family. We envision that the MMSA tool will significantly enhance the ability to interpret molecular networks, with implications for more rapid identification and prioritization of new metabolites for full characterization.