Subcellular locations of proteins are closely related to their biological function. However, a fine map of subcellular locations of proteins for liver cancer cell lines (LCCLs) has yet to be constructed. Here, we isolated six membrane-bound organelles (i.e., plasma membrane, endosome, lysosome, mitochondria, endoplasmic reticulum, and Golgi apparatus) using MinuteTM organelle isolation or enrichment kits (Invent Biotechnologies, Inc., Plymouth MN), and then used label-free proteomics technique to quantify protein in each organelle. We predicted subcellular protein locations by the combined use of organelle marker proteins and a machine learning algorithm. The database contains information on subcellular locations of proteins in Sk-hep1 cell, as well as on the interactions between members of the protein complex. Our data are easily browsed and can be downloaded via this portal. Please refer to our article for more information.