Each experiment directory contains the Thermo RAW files for all the matched matrix calibration curves (yeast_curves, csf_curves, and ffpe_curves; water_curves and hela_curves refer to the yeast reference proteome diluted in water and hela backgrounds, respectively). The folder "demultiplexed_mzml" contains the demultiplexed converted files used as input for the Skyline documents and for the EncyclopeDIA analyses. For the EncyclopeDIA outputs, please see the "Data Matrices" tab (top right).