Redox proteomics: chemical principles, methodological approaches and biological/biomedical promises

1. Introduction 2. Reactive Oxygen and Nitrogen Species 2.1. Exogenous and Endogenous Cellular Sources of ROS and RNS 2.1.1. Superoxide Anion 2.1.2. Hydrogen Peroxide and Hydroxyl Radical 2.1.3. Nitric Oxide 2.1.4. Peroxynitrite 2.1.5. Derivatives from Lipid Peroxidation 2.2. Molecular Systems Involved in the Maintenance of Cell Redox Homeostasis 2.3. Biological Effects Associated with ROS/RNS Activity 2.4. Oxidative/Nitrosative Damage and Pathological Aspects 3. Proteins as Targets of ROS/RNS Activity 3.1. Cysteine Susceptibility to Redox Reactions 3.1.1. Protein S-Glutathionylation 3.1.2. Protein S-Nitrosylation 3.2. Methionine Sulfoxidation 3.3. Protein Carbonylation 3.4. Tryptophan and Histidine Oxidation 3.5. Tyrosine and Tryptophan Nitration 3.6. Tyrosine Halogenation 4. Proteomic Analysis of Oxidized, Nitrosylated, and Nitrated Proteins 4.1. Proteomic Methods 4.2. Analysis of Protein Adducts Resulting from ROS/RNS-Induced Modifications at Cysteine 4.2.1. Analysis of Protein Adducts Resulting from Disulfide Bond Formation 4.2.2. Analysis of Protein Adducts Resulting from S-Glutathionylation 4.2.3. Analysis of Protein Adducts Resulting from Cysteine Oxidation 4.2.4. Analysis of Protein Adducts Resulting from S-Nitrosylation 4.2.5. The OxMRM Method 4.3. Analysis of Protein Adducts Resulting from ROS/RNS-Induced Modifications at Methionine 4.4. Analysis of Protein Carbonylation Products 4.4.1. Analysis of Protein Adducts Resulting from Oxidation at Lysine, Arginine, Threonine, and Proline 4.4.2. Analysis of Adducts Resulting from Protein Reaction with Lipooxidation End-Products 4.4.3. Analysis of Protein Glycooxidation End-Products 4.5. Analysis of Protein Adducts Resulting from ROS/RNS-Induced Modifications at Tyrosine 4.6. Analysis of Protein Adducts Resulting from ROS/RNS-Induced Modifications at Tryptophan and Histidine 4.6.1. Analysis of Protein Adducts Resulting from Tryptophan Oxidation 4.6.2. Analysis of Protein Adducts Resulting from Tryptophan Nitration 4.6.3. Analysis of Protein Adducts Resulting from Tryptophan Halogenation 4.6.4. Analysis of Protein Adducts Resulting from Histidine Oxidation 5. Concluding Remarks and Future Perspectives