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Among the endoproteases which could be used for protein digestion, the serine protease trypsin is most commonly employed as it generates peptides which are highly amenable to MS(/MS) analysis. Depending on the preceding workflow, the enzymatic digestion of proteins is performed either in-gel or in-solution, generally, the in-gel digestion methodology has become routine for proteins separated by 2-D electrophoresis while in-solution digestion are usually used in LC-MS/MS analysis. The protein is cut enzymatically into a limited number of shorter fragments during digestion and these fragments are called peptides and allow for the identification of the protein with their characteristic mass and pattern.Following the separation of samples by 1-D or 2-D gel electrophoresis, proteins are fixed and visualized using an MS-compatible stain, usually Coomassie Blue, or silver employing a glutaraldehyde-free protocol. Visualized proteins are excised from the gel and the respective gel bands or spots are washed for destaining and dehydrated before being trypsinized.The permeation of the enzyme to the gel is believed to be facilitated by the dehydration of the gel pieces by treatment with acetonitrile and subsequent swelling in the digestion buffer containing the protease. Different studies about the penetration of the enzymes to the gel showed the process to be almost completely driven by diffusion, by cutting the gel to pieces as small as possible the efficiency of the in-gel digestion could be achieved.
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