On the Add/Edit Modifications tab, you can add N-terminal, C-terminal, or residue-specific side-chain modifications to a seqeunce.

Prerequisites

  1. You are viewing the Theoretical Protein/Peptide Manager.

Procedure

  1. Select the Add/Edit Modifications tab in the Theoretical Protein/Peptide Manager.
  2. Add/Edit Modifications pane
    Figure Add/Edit Modifications pane
  3. Select one of the processing modes and either (or both) of the checkboxes described in the table below.
Modifications processing modes in the Theoretical Protein/Peptide Manager

Processing mode

Component generation

Parameter application

Process Sequence from Above Input Box (default)

Components in the Results table are generated using the original sequence added to the Theoretical Protein/Peptide Manager.

  • Select the Create a Copy checkbox to retain an unmodified version of each theoretical component and then apply the specified modifications to a copy of the component.
  • Clear the Create a Copy checkbox to overwrite all theoretical components with the specified modifications.

Parameters on the Add/Edit Modifications tab are globally applied to the original sequence during theoretical component generation.

Batch Process All Peptides from Results Table

To enable this processing mode, first generate theoretical components using the Process Sequence from Above Input Box (default) mode.

Then, reprocess the component results using the Batch Process All Peptides from Results Table mode.

  • Select the Create a Copy checkbox to retain an unmodified version of each theoretical component and then apply the specified modifications to a copy of the component.
  • Clear the Create a Copy checkbox to overwrite all theoretical components with the specified modifications.

Parameters on the Add/Edit Modifications tab are globally applied to theoretical components initially generated from the Process Sequence from Above Input Box (default) mode.

Process Individual Selected Peptide from Results Table

To enable this processing mode, first generate theoretical components using the Process Sequence from Above Input Box (default) mode. Then, select a component row in the Result table. The selected component appears in the adjacent read-only box.

Then, reprocess the specified component result using the Process Individual Selected Peptide from Results Table mode.

  • Select the Create a Copy checkbox to retain an unmodified version of the selected theoretical component and then apply the specified modifications to a copy of the component.
  • Clear the Create a Copy checkbox to overwrite the selected theoretical component with the specified modifications.
  • Select the Generate Transitions Using Original Peptide Parameters checkbox to generate theoretical components using the original parameters specified for the initial Process Sequence from Above Input Box (default) processing job.
  • Clear the Generate Transitions Using Original Peptide's Parameters checkbox to generate theoretical components using the current parameters only.

Parameters on the Add/Edit Modifications tab are applied to a single user-specified theoretical component initially generated from the Process Sequence from Above Input Box (default) mode.

  1. In the Modifications table, use the dropdown lists to choose a modification (if any) for the N-terminal, C-terminal, and side-chain residues in the sequence.