Nitric oxide generates reactive nitrosative species, such as peroxynitrite ($ONOO^-$) that may be involved in a number of diseases. $ONOO^-$ can mediate protein tyrosine nitration which causes structural changes of affected proteins and leads to their inactivation. Various proteomics and immunological methods including mass spectrometry combined with both liquid and 2-D PAGE, and immunodetection have been employed to identify and characterize nitrated proteins from pathological samples. This review presents the pahtobiological roles of the pathogenic posttranslational modification in neurodegenerative diseases and atherosclerosis.