Multiplexed Tandem Mass Spectrometry Imaging Enables Large-Scale Isomer Mapping and Annotation in Tissues

Accurate molecular annotation is essential for deciphering biochemical processes in spatial biology. Here, we present a scalable and broadly applicable molecular annotation tool for tandem mass spectrometry imaging (MS²I). Our workflow includes parallel image acquisition (PIA) for parallel MS²I and an open-access computational framework for spatial similarity networking (SSN) that enables molecular annotation of MS²I data with isomeric specificity. The PIA enables simultaneous untargeted MSI and targeted MS²I ensuring structure-specific imaging of hundreds of molecules in a single experiment. The SSN increases annotation confidence through graph-based spatial correlation of product ion distributions, opening up new avenues for data investigation and annotation from both MSI and MS²I data. By integrating PIA and SSN into a single workflow, we visualize and annotate 134 phospholipid isomers and isobars in mouse brain tissue. Furthermore, we demonstrate the biological utility of the platform by mapping cholesterol metabolism in human multiple sclerosis brain tissue, revealing lesion-associated cholesterol oxidation pathways. Finally, we propose annotation confidence levels for structural annotation in MSI. Overall, PIA and SSN together provide large-scale, structure-specific MSI, expanding the scope for spatial metabolomics, lipidomics, and chemical pathology through molecular annotation beyond current capabilities.