When you add a new protein sequence, you must assign a category to the sequence before saving and adding modifications.


  1. On the Sequence Editor page, select one of the following categories from the Category drop-down list to assign to the protein sequence:
  2. Peptide Mapping
  3. Top Down
  4. Intact Protein
  5. When you open a previously saved protein sequence has been assigned a Category value other than the default selections of Peptide Mapping, Intact Protein, Top Down, or Unknown, that value moves to the Description box automatically.
  6. If you import a sequence created in BioPharma Finder 2.0 or earlier, the application assigns the sequence as Unknown and adds any custom category text to the Description box. You must select an appropriate category for the sequence to be visible in the Protein Sequence table on the corresponding analysis page
  7. The category controls the functionality of some of the panes in the Protein Sequence Editor. Once you assign a category to your sequence, you can edit category-specific parameters in the Sequence Editor. Inactive parameters are not editable.
  8. If you change the category of your sequence and the change affects the functionality of a pane, you receive a prompt to confirm the category change. After you confirm the category change, the application automatically clears all of your currently specified variable modifications, maximum number of modifications, glycan, and proteoform settings. The application resets these parameters to the default values before deactivating the pane.
  9. After you assign the appropriate category to your sequence, you can define or edit the protein sequence, add appropriate modifications, and then save the sequence.