Secretome analysis is crucial to unravel extracellular processes. However, secreted proteins are difficult to detect in mass-spectrometry-based analysis due to contamination of serum proteins deriving from cell culture media and to high glycosylation, which hampers tryptic digestion. Secret3D workflow is an optimized protocol for the global analysis of secretome from in vitro cultured cells. It allows efficient and robust protein identification and quantitation and provides information on putative N-glycosylation sites of the secreted proteins. For complete details on the use and execution of this protocol, please refer to Matafora et al. (2020).