Add/edit modifications - BioPharma Finder Software - Add/edit modifications - BioPharma Finder Software - BioPharma Finder Software

Procedure

1. On the Theoretical Protein/Peptide Manager page, select the Add/Edit Modifications tab.
2. The Add/Edit Modifications pane opens, displaying the processing parameters.

3. 

2. Select one of the processing mode options:
1. Process Sequence from Above Input Box (default)
2. Batch Process All Peptides from Results Table
3. Process Individual Selected Peptide from Results Table
4. The modification parameters apply globally to the original protein/peptide sequence that was entered, globally to all of the processed peptides in the Results table, or locally to one selected peptide in the Results table, depending on the selected mode.
5. Local modifications overwrite previous global modifications. Global modifications do not overwrite previous local modifications
6. For more information on these processing modes, see Add/edit target m/z parameters.
3. In the modifications table, select a modification for the N- and C-terminals and amino acid letters, as needed.
4. By convention, the peptides are written from the N-terminal (free amine group of the first amino acid) to the C-terminal (free carboxylic group of the last amino acid).
5. For the first two processing modes (Process Sequence from Above Input Box or Batch Process All Peptides from Results Table), the modifications table displays all amino acid letters and the N-terminal and C-terminal. The letters appear in the order listed in the amino acids table. See Amino acid letter codes.

6. 

7. For the third processing mode (Process Individual Selected Peptide from Results Table), the modifications table displays the N-terminal, all amino acid letters in the selected peptide, and then the C-terminal. The letters appear in the order that they appear in the selected peptide.

8. 

9. If the selected protein/peptide already contains some modifications, these modification appear in the modifications table.
10. In the Modification column of the table, a drop-down list displays all available modifications for each terminal or letter.
11. For the first two modes, each selected modification applies to all instances of the corresponding letter in the original sequence or processed peptides.
12. For the third mode, each selected modification applies to only one instance of the corresponding letter in the selected peptide.
4. Select the Create a Copy checkbox, the Generate Transitions Using Original Peptide's Parameters checkbox (third mode only), or both (third mode only).
1. (For the first and second modes) Select the Create a Copy checkbox to create and retain an original, unmodified version for all peptides, and then apply the specified modifications to a new copy of each of these peptides. Clear the Create a Copy checkbox to overwrite all current peptides with the specified modifications.
2. (For the third mode) Select the Create a Copy checkbox to save a version of the currently selected peptide and then apply the specified modifications to a new copy of this peptide. Clear the Create a Copy box to overwrite the currently selected peptide with the specified modifications.
3. (For the third mode) Select the Generate Transitions Using Original Peptide Parameters checkbox to generate the transitions for the selected peptide using the parameter settings applied to its original version, not from any current parameter settings. Clear the Generate Transitions Using Original Peptide's Parameters checkbox to generate the transitions for the selected peptide using the current parameter settings.
5. When you are finished specifying the parameters, select Process.
6. The Results table displays the results of the theoretical experiment.
7. See Results table parameters.
6. When you are finished, you can save your results as a data file (.msqc), export peptides as a Microsoft® Excel worksheet® (.xslx) or BioPharma Finder file (.bpf), and save selected peptides as a peptide workbook using the buttons on the command bar.
7. See Use a Chromeleon-compatible workbook.