**3. Conclusion**

Two-dimensional gel electrophoresis and MALDI-MS are an effective strategy for determining the protein domains present in those gel spots that are observed at significantly lower MW values than are given in the database. While average sequence coverage is only 30%, the peptides detected are confined to a specific region of the protein, such as the protein N- or Cterminal. This information could easily be incorporated into protein identification tables. Regional coverage information is not readily available from either LC-MS/MS analysis of digests of cellular lysates or from epitope-specific antibodies. Some of the protein fragments correspond to chains produced by known cellular processing and activation pathways. Others have been detected as functional and structural domains during in vitro experiments or noted in other in vivo studies, indicating they function intra- or extra-cellularly. By using tools that allow both protein identification and measurement of MW, we can assess the abundance and distribution of protein fragments. Correlation of these results with targeted functional studies on specific proteins will elucidate the biological function of protein fragments.

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**Part 7** 

**Other Applications of** 

**Gel Electrophoresis Technique** 

