Highly Multiplexed TAG-Mass MALDI-MSI Dataset for Spatial Immune Profiling of Breast Tumors

Dataset description (MALDI-MSI TAG-mass panel): This dataset contains MALDI mass spectrometry imaging (MSI) data acquired across multiple acquisition cycles, where each cycle corresponds to a panel of antibody-derived mass tags (TAGs). Each immunohistochemical marker is conjugated to a unique mass reporter, allowing multiplexed detection through its specific mass-to-charge ratio (m/z). For each cycle: Cycle 1 includes markers such as CD4 (m/z 192.266), CD8 (215.200), FoxP3 (189.185), PD-L1 (203.222), and Ki67 (245.293), targeting T-cell populations, immune checkpoints, and proliferation. Cycle 2 focuses on co-stimulatory and regulatory receptors, including CD28 (189.215), CD40 (192.266), OX40 (217.279), and CTLA4 (231.246). Cycle 3 captures antigen presentation and exhaustion-related markers such as MHC I (215.200), MHC II (219.252), LAG3 (192.266), and HLA-E (245.293). Cycle 4 includes activation and inhibitory receptors such as CD137/4-1BB (231.286), NKG2A (192.266), and TIGIT (233.337). Cycle 5 contains markers related to immune regulation and suppression, including CD154/CD40L (219.315), VISTA (205.273), and IDO II (245.310). Each m/z value uniquely identifies a tagged antibody, enabling spatially resolved detection of marker expression in tissue sections. Prognostic annotations (good, neutral, or bad) and biological mechanisms associated with each marker are also provided in the table to facilitate biological interpretation. The imzML files deposited here correspond to individual acquisition cycles, and users can reference the provided marker–m/z mapping table to interpret ion images and reconstruct multiplexed protein distributions.