Updated publication reference for PubMed record(s): 31768060. We have developed DIA-NN, an integrated software suite for fully-automated processing of raw SWATH/DIA data. DIA-NN enables deep and confident proteome coverage with fast chromatographic methods, paving the way for a new generation of high-throughput proteomics. This data set illustrates the capabilities of DIA-NN when analysing microflow SWATH data acquired with 19 - 23 minute gradients as well as the use of DIA-NN to generate spectral libraries directly from SWATH/DIA data.