We performed quantitative proteomic profiling of 786 plasma samples from COVID-19 inpatients, treated at two different hospitals (Charité – Universitätsmedizin Berlin and University Hospital of Innsbruck). Sampling was performed at multiple time points throughout the course of the disease, to create a time-resolved map of COVID-19 progression. Full DIA-NN analysis reports are provided, as well as raw files for the QC runs.