Reactive oxygen and nitrogen species can modify various biomolecules, including proteins. The resulting protein modifications are highly diverse, can be reversible as well as irreversible, and might affect protein structure and function. Besides random modifications, targeted modifications at specific amino acids in surface-accessible protein regions occur. These changes are of particular interest as, e.g. by altering the local protein conformation; they might initiate specific (oxidative) signaling pathways. Here, we focus on two protein modifications that are found under conditions of oxidative stress in plants: oxidation of the sulfur-containing methionine and nitration of tyrosine. We review the functional consequences caused by the oxidation of several plant proteins and line-up those proteomics technologies that are amenable to study these selected modifications.