You can specify the charge state and m/z ranges and the maximum number of isotopes that the application uses for predicting theoretical peptides.

Procedure

  1. On the Theoretical Protein/Peptide Manager page, select the Add/Edit Target m/z tab.
  2. The Add/Edit Target m/z pane opens, displaying the processing parameters.
  3. Add/Edit Target m/z pane
    Add/Edit Target m/z pane
  4. Select one of the processing mode options:
  5. Process Sequence from Above Input Box (default)
  6. For this option, when you process the transitions, all of the target m/z parameters apply globally to the original protein or peptide sequence in the Sequence area of the Theoretical Protein/Peptide Manager page.
  7. Batch Process All Peptides from Results Table
  8. To enable this option, process the transitions at least once to generate the peptides in the Results table on the right side of the Theoretical Protein/Peptide Manager page.
  9. For this option, when you process the transitions again, all of the target m/z parameters apply globally to all of the processed peptides in the Results table
  10. Process Individual Selected Peptide from Results Table
  11. To enable this option, after processing the transitions at least once, select one peptide row in the Results table on the right side of the Theoretical Protein/Peptide Manager page.
  12. This action switches from the other options to the Process Individual Selected Peptide from Results Table option and displays the selected peptide in the adjacent box. This box is not editable.
  13. For this option, when you process the transitions again, all of the target m/z parameters apply locally to only the selected peptide.
  14. image/svg+xml Peptide that you selected in the results table to the right
    Process Individual Selected Peptide from Results Table option with selected peptide shown
  15. In the Charge State Range boxes, specify the lower and upper values for the range of charge states to be used for the prediction.
  16. In the Number of Isotopes box, specify the number of isotopes that you want returned from the prediction of each charge state.

  17. NOTE

    To ensure that the processed results are compatible with the Chromeleon™ chromatography data system, limit the range of isotopes to between three and five.

  18. In the m/z Range boxes, type the lower and upper values for the m/z range for the prediction.
  19. To perform the theoretical experiment without changing the default Add/Edit Modifications, select Process.
  20. The Results table displays the results of the theoretical experiment.
  21. See Results table parameters.
  22. Otherwise, you can edit the Add/Edit Modifications before processing, as necessary.
  23. See Add/edit modifications.