To determine the location of a protein-ligand interface, for example, it is necessary to probe separately the solvent-exposed side-chains of the protein alone and of the protein-ligand complex. Side-chains that are modified in the protein alone, and not in the complex, indicate areas of decreased solvent accessibility due to ligand binding. After the protein is modified, standard proteomic analytical methods can be applied to pinpoint the oxidized amino acids by comparing the product-ion spectra of the unmodified peptides with those of oxidized peptides. Most oxidations can be located by searching for peptides whose m/z values are +16, +32, +48, —22 or +5 Da compared to those of the parent ion. These mass shifts correspond to addition of one, two or three oxygens to any residue, except for histidine, which undergoes other side-reactions to afford mainly +5 and —22 end-products.
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