Proteomics refers to the analysis of the complete complement of proteins expressed in a given set of cells, biological fluids (e.g., plasma, urine, saliva), tissues and organs (e.g., brain slices, liver), or whole organisms. Proteins are extracted from these sources and are digested into peptides using enzymes. Because of the complexity of the peptide mixture, multiple dimensions of liquid chromatographic or other separation techniques are used to separate the peptides. The final liquid chromatography separation is coupled to mass spectrometry analysis, where the intact masses of peptides are measured as well as their corresponding gas-phase fragments. Using sophisticated database searching algorithms, the raw data is searched against species-specific databases to give the identification of proteins present in the mixture. Our laboratory specializes in developing high-throughput quantitative proteomics workflows that allow for sample multiplexing. Sample multiplexing is achieved using chemical tagging strategies and our methods are readily adopted to study oxidative post-translational modifications of proteins. We recently have begun to automate aspects of our workflow to further increase sample throughput.