Schematic diagram for the relative quantification of the redox state of cysteine-containing peptides between two samples. Each sample (control and test) is split in two. One set has its free thiols initially blocked with the alkylating reagent NEM. Once excess NEM is removed, all samples have their reversibly oxidized thiols reduced with DTT. Free thiols in all samples are then labeled with thiol-specific biotin-HPDP, and protein concentration is measured so all samples have equivalent protein content. Proteins are tryptic digested and peptides labeled with iTRAQ reporter tags according to the scheme outlined. Labeled peptides are combined. Biotinylated cysteine-containing peptides are purified using streptavidin, and purified peptides are analysed and quantified by MS/MS.