Tyrosine nitration is a common post-translational modification affecting protein structure and function. It is based on the addition of a NO2 group at the ortho position of the phenolic hydroxyl group of tyrosine to yield 3-nitrotyrosine (3-NTyr). Understanding how tyrosine nitration affects the structure and functionality of proteins is of considerable interest, as it is associated with pathogenesis in diseases related to oxidative stress in all living organisms. There are several methods to nitrate tyrosine residues in native proteins. Among them, nitration by the chemical agent peroxynitrite stands out for its biological relevance. Recently, a genetically evolved suppressor tRNA has been developed to provide in vivo incorporation of 3-NTyr into proteins. In this minireview, we discuss the advantages and limitations of these chemical and biological methods and propose a non-damaging method to analyze the configuration and dynamics of nitrotyrosine residues in native proteins by NMR spectroscopy.