Mitochondria play a central role in redox-linked processes in the cell through mechanisms that are thought to involve modification of specific protein thiols, but this has proved difficult to assess. In particular, specific labeling and quantitation of mitochondrial protein cysteine residues have not been achieved due to the lack of reagents available that can be applied to the intact organelle or cell. To overcome these problems we have used a combination of mitochondrial proteomics and targeted labeling of mitochondrial thiols using a novel compound, (4-iodobutyl)triphenylphosphonium (IBTP). This lipophilic cation is accumulated by mitochondria and yields stable thioether adducts in a thiol-specific reaction. The selective uptake into mitochondria, due to the large membrane potential across the inner membrane, and the high pH of the matrix results in specific labeling of mitochondrial protein thiols by IBTP. Individual mitochondrial proteins that changed thiol redox state following oxidative stress could then be identified by their decreased reaction with IBTP and isolated by two-dimensional electrophoresis. We demonstrate the selectivity of IBTP labeling and use it to show that glutathione oxidation and exposure to an S-nitrosothiol or to peroxynitrite cause extensive redox changes to mitochondrial thiol proteins. In conjunction with blue native gel electrophoresis, we used IBTP labeling to demonstrate that thiols are exposed on the matrix faces of respiratory Complexes I, II, and IV. This novel approach enables measurement of the thiol redox state of individual mitochondrial proteins during oxidative stress and cell death. In addition the methodology has the potential to identify novel redox-dependent modulation of mitochondrial proteins.Changes in the thiol redox state of mitochondrial proteins are significant in a number of cellular processes including the permeability transition, cell death due to calcium loading and oxidative stress, the response of cells to nitric oxide, tumor necrosis factor signaling, commitment to apoptosis, and in regulating respiratory chain function (1-9). However the detailed mechanisms and the proteins involved are uncertain. This is partly because of the technical challenges presented by determining thiol modifications of proteins in general and the difficulties inherent in mitochondrial proteomics. Potential protein thiol alterations include formation of mixed disulfides or internal disulfides from vicinal dithiols, S-nitrosation, and the formation of higher oxidation states (10 -15). The differential reactivity of individual protein thiols and the range of lifetimes of altered redox states can act as signal sensors or transducers to influence mitochondrial function (13-17). Nitric oxide may be a particularly important regulator of mitochondrial protein thiols because it diffuses easily into mitochondria and partitions selectively into the lipid bilayer where it can modify otherwise inaccessible thiols (18 -20). Modification of protein thiols by nitric oxide most likely occurs...