HIT-MAP: A Scalable Approach to Multimodal Mapping of Subcellular Organization

Multimodal mapping of subcellular protein organization through imaging and interaction proteomics has been mostly confined to large consortia, owing to high per-target costs, reliance on target-specific antibodies or libraries of epitope-tagged cDNAs, and the lack of unified pipelines for coordinated data acquisition. Here, we present HIT-MAP (high-throughput integrated tagging for cell mapping), an end-to-end framework that couples endogenous epitope tagging with optimized wide-field immunofluorescence imaging and affinity purification-mass spectrometry (AP-MS). Applied to a pilot set of 16 representative proteins in HEK293T cells, HIT-MAP recovers 576 high-confidence protein-protein interactions, identifies canonical complexes, and resolves cross-modality protein communities. Integrative analysis identifies CCDC12 as a previously uncharacterized component of the Bact spliceosomal compl…