Selenium is one of the indispensable trace elements for human health and its dominant form in human body is selenocysteine,which serves as critical active-site residues in selenoproteins in regulating redox balance.Selenium excess and deficiency are both implicated with severe diseases.However,it remains challenging to profile selenoproteins by traditional shotgun proteomics tools due to its low abundance and versatile activity states.We have developed a computational program to detect the characteristic isotope envelope of selenium-containing peptides from complex proteomic data and use the information to guide the proteomic analysis in a targeted mode.We showed that the method can dramatically improve the sensitivity of detecting natural selenoproteins in cellular and tissue proteomes.Our selenium-encoded chemical proteomic strategy will be a novel tool and great resource for in-depth proteomic analysis of selenoproteins and other selenium-containing biomolecules,which will aid functional studies of selenoproteins and their implications in human health.