When you select the Perform Digestion checkbox at the top right of the Enter Peptide or Protein Sequence area of the Theoretical Protein/Peptide Manager, the application activates the Digestion Parameters tab where you can specify the protease, peptide length constraints, and number of missed cleavage sites allowed for the theoretical digestion.

Prerequisites

  1. You are viewing the Theoretical Protein/Peptide Manager.
  2. You selected the Perform Digestion checkbox.

Procedure

  1. Select the Digestion Parameters tab in the Theoretical Protein/Peptide Manager.
  2. Digestion Parameters (optional) pane
    Figure Digestion Parameters (optional) pane
  3. In the Select Protease area, select a protease to apply to the digestion.
  4. The activities at the N-terminal and C-terminal for the selected protease appear in the N-Term and C-Term boxes, but are not editable.

  5. TIP

    The list of proteases in the Theoretical Protein/Peptide Manager corresponds to the proteases available in the Peptide Mapping Analysis workflow.

    To add a new protease or edit protease parameters, use the Identification page of the processing method editing wizard in the Peptide Mapping Analysis workflow.

  6. In the Peptide Length Constraints boxes, specify the lower and upper values for the peptide length range.
  7. In the Number of Allowed Missed Cleavage Sites box, specify the maximum number of internal cleavage sites within a peptide fragment that a protease can miss during the digestion process.