Updated project metadata. The Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics for global profiling analysis of protein subcellular localization. Here, we have drastically enhanced the performance of DOMs through data-independent acquisition (DIA) mass spectrometry (MS). DIA-DOMs achieve twice the depth of our previous workflow in the same MS runtime, and substantially improve profiling precision and reproducibility. This repository contains all DDA-LFQ datasets used in our work: A reference dataset acquired in single shot on 100 min gradients and three fractionated datasets providing measured libraries for DIA searches on 100 min, 44 min and 21 min gradients.