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

Prerequisites

1. You are editing a protein sequence in the Protein Sequence Editor.
2. The sequence has the "Peptide Mapping" category for Peptide Mapping Analysis or the "Intact Protein" category for Intact Mass Analysis.

Procedure

1. In the Protein Sequence Editor, expand the Variable Modifications for Intact and Peptide Analysis pane on the right side of the page.
2. At the top of the pane, in the Max # Modifications area, type the maximum number of modifications the application can apply to the sequence during Intact Mass Analysis (Intact Protein box) or Peptide Mapping Analysis (Peptide Mapping box).
3. For Intact Mass Analysis, the maximum number of modifications is 10.
4. For Peptide Mapping Analysis, the maximum number of modifications is 8.
5. The maximum number of modifications does not include glycosylations.

6. IMPORTANT

   Setting the "Max # of Modifications" parameter to a high value greatly increases the possible combinations of modifications in the sequence which might prolong job processing time.

3. Next, add variable N-terminal, C-terminal, and side-chain modifications from the Modifications lists (left) to the Modifications Selected for Search lists (right):
1. To assign a modification, select it from the Modifications list, and then select the Add button.
2. To remove a modification, select it from the Modifications Selected for Search list, and then select the Remove button.
3. To quickly assign all modifications in the default sublist, select the Load Default Mods button.
4. Continue adding modifications from the Modifications list (left) to the Modifications Selected for Search lists (right) as necessary.

5. 

5. Save the protein sequence.