Recent studies of crystallins and cytoskeletal proteins confirm that proteolytic modification of lens proteins occur during the earliest stages of lens development. Prior to these studies, it was widely accepted that protein modification in lens proteins was primarily related to aggregation and cataract formation. Proteolytic processing of cytoskeletal proteins, lens specific filaments, crystallins, and enzymes may contribute to organization of transparent structures in lens cells. Innovations in mass spectrometry provide new methods for characterization of protein modifications during normal development and differentiation in young lens and during the loss of transparency in aging lenses. Methods are available to provide high throughput identification and sequencing of proteins isolated from 2-D SDS-PAGE making possible a systematic analysis of the total expressed proteins of the lens. These analyses will be extended to normal and cataractous young and old human lenses. By undertaking a systematic analysis of lens proteins, we have the opportunity to make correlations between specific proteolytic modifications and the transparent condition of lenses.