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

This is the authors' abstract. We don't add key points for this paper.

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 complex, supported by AP-MS interaction data, tag-free size-exclusion chromatography-mass spectrometry (SEC-MS) co-fractionation, and Perturb-seq transcriptional signatures. HIT-MAP lowers technical and economic barriers to generating coordinated multimodal protein maps.