MS raw data and converted, aligned CSV files are uploaded, including single-cell MS data from circulating tumor cells (CTCs) and primary tumor cells. CTCs were isolated by fluorescence-activated cell sorting (FACs) from 38 cancer patients with multiple solid tumor types, including hepatoblastoma (HB), neuroblastoma (NB), nephroblastoma (NPB), and pancreatic cancer (PC). Single cells from the patient’s surgical resected tissues were also sampled and described as “Tissue” in this study.