Assign static modifications - BioPharma Finder Software - Assign static modifications - BioPharma Finder Software - BioPharma Finder Software

Procedure

1. In the Protein Sequence Map pane of the Protein Sequence Editor, position the cursor to the left of one of the following amino acid letter codes:
1. For a side chain modification, the side chain residue of interest.
2. For an N-terminal modification, the first residue of the chain.
3. For a C-terminal modification, the last residue of the chain.
2. Then, double-click.
3. The Residue Properties and Modifications dialog box opens.
4. The properties of the selected amino acid appear in the Residue Properties area. Check these properties to make sure that you selected the appropriate amino acid.

5. 

6. NOTE

   You can not assign any static modifications to a disulfide-linked cysteine (C) residue.

3. (Optional) To assign any side chain modifications, in the Side Chain Modification area, select a modification from the drop-down list to assign the modification to the specified residue.
4. The monoisotopic mass of the selected modification appears in the Mono. Mass box.
5. The average mass of the selected modification appears in the Avg. Mass box.
6. The application assumes the new m/z value for this amino acid when you process an experiment involving the modified protein sequence.
4. (Optional) To apply the side chain modification to all residues of the selected amino acid, select the Apply to All checkbox.
5. When you add a static modification to a side chain, the modified amino acid is highlighted in blue in the Protein Sequence Map.
6. If you selected Apply to All for a side-chain modification, all of the instances of the modified amino acid are highlighted in blue.

7. TIP

   For efficiency, if you want to apply a modification to most of the instances of an amino acid in a side-chain, select the Apply to All checkbox and then select OK.

   Then, repeats steps 1 and 2 above, selecting the particular residues that you do not want to modify. Select None from the drop-down list of modifications or select the Clear button to removes the modification for that particular instance of residue.

5. (Optional) To assign any N- or C-terminal modifications, in the N- (or C-) Terminal Modification area, select the modification from the list to assign the modification to the to N- or C-terminal of the chain and select OK.
6. When you add a static modification to the N-terminal or C-terminal, the modified amino acid is highlighted in blue in the Protein Sequence Map.
7. The monoisotopic mass of the selected modification appears in the Mono. Mass box.
8. The average mass of the selected modification appears in the Avg. Mass box.
9. The application assumes the new m/z value for this amino acid when you process an experiment involving the modified protein sequence.
6. (Optional) Repeat the previous steps to assign side chain, N-terminal, or C-terminal modifications to any other chains of interest.

7. 

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.