This protocol details steps in discovery proteomic data-independent acquisition with a standard-flow UHPLC-Obitrap system and a subsequent DIA-NN library-free database search. The data acquisition method was adapted from González Fernández-Niño, S. M., et al. "Standard flow liquid chromatography for shotgun proteomics in bioenergy research."Frontiers in bioengineering and biotechnology, 3 (2015): 44.