Both gel-based (one-dimensional [1D] gel electrophoresis, two-dimensional [2D] polyacrylamide gel electrophoresis, 2D difference in-gel electrophoresis [DIGE]) and gel-free (liquid chromatography [LC], capillary electrophoresis) approaches have been developed and utilized in a variety of combinations to separate proteins prior to mass spectrometric analysis. The typical proteomics experiment require of four steps.
Step 1: proteins isolated from cell lysate, body fluid or tissues were separated by both gel based and gel free methods.
Step 2: proteins were enzymatically digested to peptides
Step 3: peptides were analized by either ESI or MADI-MS mass spectrometer.
Step 4: mass spectra of the peptides were matched against protein sequence databases for protein identification.
