Proteomics is the study of proteomes, which are the collections of proteins expressed in cells. Whereas genomes are essentially invariant in different cells in an organism, proteomes vary from cell to cell, with time and as a function of environmental stimuli and stress. The integration of new mass spectrometry (MS) methods, data analysis algorithms, and information from databases of protein and gene sequences has enabled the characterization of proteomes. Many environmental agents directly or indirectly generate reactive electrophiles that covalently modify proteins. Although considerable evidence supports a key role for protein adducts in adverse effects of chemicals, limitations in analytical technology have slowed progress in this area. New applications of liquid chromatography-tandem mass spectrometry (LC-MS-MS) now offer the potential to identify protein targets of reactive electrophiles and to map adducts at the level of amino acid sequence. Use of the data-analysis tools Sequest and SALSA (Scoring Algorithm for Spectral Analysis) together with LC-MS-MS analyses of protein digests enables the identification of modified forms of proteins in a sample. These approaches can map adducts to specific amino acids in protein targets and are being adapted to searches for protein adducts in complex proteomes. These tools will facilitate the identification of new biomarkers of chemical exposure and studies of mechanisms by which protein modifications contribute to the adverse effects of environmental exposures.