Do you use only trypsin to digest proteins or can other proteolytic enzymes be used?
If sample is to be “in-solution digested,” we can use any one or combination of commercially available sequencing-grade proteolytic enzymes. For “in-gel digestion", the repertoire of the proteolytic enzymes becomes slightly more limited. Note that many high molecular weight enzymes are not as efficient for in-gel digestion as trypsin and chymotrypsin.
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