Assign variable modifications - BioPharma Finder Software - Assign variable modifications - BioPharma Finder Software - BioPharma Finder Software

Procedure

1. In the Oligonucleotide Sequence Editor, select the title bar for Assign Variable Modifications.
2. On the left side of the pane, the Modifications area shows all of the default variable modifications (in the 5'-Terminal, 3'-Terminal, and Oligo Variable Modification boxes) that you can apply to your sequence.
3. On the right side of the pane, the Modifications Selected for Search area shows all of the loaded variable modifications to be applied to the experiment.
4. You can edit and customize the displayed lists of default modifications as appropriate.
5. See Change the default modifications for oligonucleotide sequences.
6. You can also apply custom modifications or oligo building blocks to your sequence.
7. See Assign custom building blocks to an oligonucleotide sequence and Manage custom modifications and building blocks for oligonucleotides.
2. In the Max # Modifications area, type a value for the maximum number of modifications to assign to the sequence for oligonucleotide analysis.
3. You can assign up to eight modifications to a sequence.
4. Setting the maximum number of modifications to a high value can greatly increase the number of combinations and the search time.
3. For sequences assigned the Intact Deconvolution category, enter the appropriate specifications in the Terminal Truncation Search area:
1. Enable Search: Yes or No (default)
2. Specificity: Remove from 5' (default) or Remove from 3''
3. Lower Mass Limit: 1,000 (default); range = 1 to 100,000 (integer values only)

4. NOTE

   The Terminal Truncation Search feature applies to single-chain oligonucleotide sequences.

   If the Terminal Truncation Search feature is enabled for an oligonucleotide with multiple chains, an error message will appear upon saving the sequence.

4. In the 5'-Terminal, 3'-Terminal, and Oligo Variable Modification boxes, do the following:
1. To quickly load the modifications from the default sublist, select Load Default Mods.
2. You can edit the default sublist of variable modifications used for quick loading.
3. See Change the default modifications for oligonucleotide sequences.
1. To assign another modification, select it from the Modifications lists (on the left side), and select Add.
2. You can assign more than one modification to your sequence, but you can only select one modification at a time.
5. Continue adding modifications from the Modifications list (left) to the Modifications Selected for Search lists (right) as necessary.

6. 

6. If you want to remove a loaded modification from the Modifications Selected for Search lists, select the modification and select Remove.
7. Select Save or Save as New in the command bar to save the modifications. Or, if you do not want to save the modifications to the sequence, select Cancel.
8. See Save an oligonucleotide sequence.