This project contains the raw proteomic files (.raw) of membraneless organelles (MLOs) obtained using the Phase-APEX2-MS technique. Phase-APEX2-MS is a newly developed, photo-activatable, and highly specific proximity labeling method for targeting MLOs. It enables the proteomic analysis of specific MLOs within living cells in just 120 seconds. The technique shows high specificity, allowing for the capture of core MLO components while significantly minimizing interference from other cellular compartments. The project includes four datasets, corresponding to batches 1 to 4 mentioned in the publication, which cover two types of MLOs: the nucleolus and stress granules. The data acquisition instruments and experimental procedures for each dataset are described in the "Methods" section of the paper.