A peptide workbook is a list of peptides selected from the results on the Theoretical Protein/Peptide Manager page (or the Results table of a peptide mapping analysis experiment) and the method parameters used to process those results. You can save selected results to a peptide workbook to run a targeted peptide mapping analysis experiment or for use in the Chromeleon™ chromatography data system.


  1. On the Theoretical Protein/Peptide Manager page, select the checkbox in the row of each component in the table that you want to save to a workbook.
  2. TIP

    To select all of the rows, select the checkbox in the column header.

  3. Select Save As Peptide Workbook on the command bar.
  4. Select one of the following submenu commands:
  5. All to export all results to a workbook.
  6. Checked to export only the selected results to a workbook.
  7. The application does not support saving components with unspecified modifications, dimers, adducts, disulfide bonds, or any type of gas phase modifications to the workbook.
  8. You must clear the checkboxes for these components to save the workbook.
  9. The Save Peptide Workbook As dialog box opens.
  10. In the Save Peptide Workbook As dialog box, select one of the following options:
  11. Create a New Peptide Workbook
  12. Select an Existing Workbook
  13. (For the Create a New Peptide Workbook option) In the Workbook Name box, type a new name to create a new workbook or keep the same name to overwrite the workbook if it already exists.
  14. The default workbook name is the same as the experiment name.
  15. Use only alphanumeric, space, underscore "_", and period "." characters in the workbook name.
  16. (For the Select an Existing Workbook option) Select the checkbox for an existing workbook in the table.
  17. The application adds data from your selection of components to that workbook.
  18. A peptide workbook can contain added data from multiple different experiments.
  19. (Optional) In the Description box, type a description for the workbook.
  20. In the Number of Isotopes per Peptide box, specify the number of isotopes for the selected components.
  21. Select Save.
  22. image/svg+xml
    Save Peptide Workbook As dialog box
  23. If the workbook is currently open for editing on the Workbook Editor page, indicate whether you want the application to automatically close the open workbook before saving.
  24. The application saves all selected and identified components (but not the unidentified components) to the indicated workbook.
  25. If you are creating a new workbook, the following occurs:
  26. •Multiple peptide components with the same set of data—identification, sequence, modification, site, theoretical monoisotopic mass (within a tolerance that is ± 10 ppm of each other), protein name, and retention time (RT) (within a tolerance that is ± half of the typical chromatographic peak width for the experiment)—merge into one entry in the workbook. However, the merged entry saves the charge state distribution from the individual components.
  27. •The application automatically assigns a relative quantitation group number to all workbook entries with the same protein and sequence, starting with group number "1" and incrementing by one for each new group.
  28. If you are adding to an existing workbook, the following occurs:
  29. •The application does not merge the added components that have the same data as the components already existing in the workbook. In this case, application inserts the added components to the workbook as duplicates.
  30. •The application automatically adjusts the relative quantitation group number. The added entries with the same protein and sequence as some existing entries in the workbook receive the same relative quantitation group number as the existing entries. All other added entries receive incremented group numbers.
  31. After saving, you can manage the workbook using the Target Peptide Workbook page.
  32. See Use a Chromeleon-compatible workbook.