Trypsin digestion (PDF)
Mostly used for LC-MS/MS and structural proteomics
Chymotrypsin digestion (PDF)
You may need to think about it if trypsin doesn’t give good coverage
In gel digestion following SDS-PAGE, Blue native gel
Convenient for protein identification (ID)
Digestion Cocktail
Trypsin and partial digestion of chymotrypsin, replicability issues.