Create custom variable modifications - BioPharma Finder Software - Intact Mass Analysis User Guide - Assign modifications to a protein sequence - Create custom variable modifications - Create protein sequences - Manage variable modifications - BioPharma Finder Software - BioPharma Finder Software

Prerequisites

1. You are viewing the Protein Sequence Editor.

Procedure

1. In the Protein Sequence Editor, expand the Modification Editor pane on the right side of the page.
2. The Modification Editor looks similar to the Variable Modifications for Intact and Peptide Analysis pane and contains lists of the standard N-terminal, C-terminal, and side-chain modifications that can be modified to create custom modifications.
2. To create a new custom modification, select the Add button in the N-terminal, C-terminal, or side-chain section as appropriate.
3. The Add New Modification dialog box opens.
3. In the Add New Modification dialog box, enter the following parameters:
1. In the Name box, enter a unique name for the modification.
2. (For side-chain modifications only) In the Residues box, enter the applicable residues using the appropriate one-letter amino acid code(s).
3. In the Monoisotopic Mass and the Average Mass boxes, enter the appropriate values for the modification.

4. TIP

   If your modification involves a loss of mass, enter negative (−) mass values.

1. (Optional) In the Formula box, enter the chemical formula for the modification.

2. NOTE

   Specifying the formula for a custom modification is optional; however, if you enter a formula, it must match the entered mass values.

3. TIP

   If a custom modification involves a loss of an element or chemical group, indicate the loss using a hyphen (−) before the eliminated element or group in the Formula box.

   For example, "F−OH" specifies the addition of a fluorine atom (F) and the loss of a hydroxyl group (OH).

4. Select the OK button.
5. The modification is added to the appropriate Modifications lists in the Variable Modifications for Intact and Peptide Analysis and Modification Editor panes.

6. TIP

   Custom modifications appear in bolded purple font in the Modifications lists.

5. To delete a custom modification, select the modification in the Modification Editor pane and select the Delete button.
6. The modification is removed from the Modifications lists in the Variable Modifications for Intact and Peptide Analysis and Modification Editor panes.