which enzyme should I select? - (Feb/14/2006 )

After 2-DGE, we excised the spots, digested with trypsin and then extract the peptide for MOLDI-TOF. When searching in a database, we could not receive the expected results. So we analyzed the components of typical proteins in NCBI with the PeptideCutter service in ExPASy. And we concluded that trypsin digestion was not suited to be employed in protein identification for these proteins have a very low arginine and lysine content.

I found that Chymotrypsin might be proper, but it cleavage sites are variable. According your experance, could I use it?

thanks!

i never tried it but i know it cuts phe/tyr/trp/leu....mainly bulky non-polar, aromatic residues....you mean sometimes it cuts other also?
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I am sorry. I mean that the cleavage probability is different between different site.

Could you be kind enough to give me some suggestion?

Thanks!