Multiplexed ion beam imaging by time-of-flight (MIBI-TOF) workflow. Tissues are first labeled with a multiplex panel of antibodies conjugated with heavy metals containing polymers. Next, these are directly ionized to generate secondary ions. Ions are filtered and detected by time-of flight mass spectrometry. Next, multiplex images are generated, containing images depicting expressions for each separate antibody–metal conjugate. These images can be processed into single-cell expression data. During imaging analysis, these images can be processed into single-cell expression data and downstream analysis is performed (e.g., cell type mapping, clustering, marker expression).