You can export data in the result file to Excel workbooks, including hierarchical data in three layers—for example, proteins (layer 1), their connected peptides (layer 2), and their connected PSMs (layer 3). You can select which data to export on each level from all the visible results on a result file page.

The application supports the Excel .xlsx format. It exports only rows that are not filtered out by the current row filter. When you select the Excluded Items Only option, the application applies the filter to excluded items.

Procedure

  1. Open your search results in the result file. See Organizing results.
  2. Select File > Export > To Microsoft Excel.
  3. The Export to Excel dialog box opens.
  4. Export to Excel dialog box exporting proteins, peptide groups, and PSMs
    Export to Excel dialog box exporting proteins, peptide groups, and PSMs
  5. In the Path box, enter the path and name of the file where you want to save the Excel workbook; or locate the file, select it, and select Save in the Save As dialog box.
  6. In the Items and Associated Tables To Be Exported area, select the items to export:
  7. In the Level 1 list, select the page of the result file to export.
  8. The Level 2 checkbox becomes available.
  9. (Optional) Select the Level 2 checkbox, and then select from the list the page associated with the result page that you selected in the Level 1 list.
  10. The Level 3 checkbox becomes available.
  11. (Optional) Select the Level 3 checkbox, and then select from the list the page associated with the result page that you selected in the Level 2 list.
  12. To export only certain data on the pages that you selected in the Items and Associated Tables To Be Exported area, do the following:
  13. On the appropriate pages of the result file and their associated pages, select the checkbox in the Checked column to the left of each row to export.
  14. For information, see Check items on the pages of a result file.
  15. In the Options area of the dialog box, select the Checked Items Only checkbox.
  16. Otherwise, the application exports all data on the pages that you selected.
  17. To export only the items that were excluded in the report processing, do the following:

  18. NOTE

    Excluded items are those that you filtered out with the settings of the Peptide And Protein Filter node. For more information, see Peptide and Protein Filter node.

  19. On the appropriate pages of the result file and their associated pages, select the checkbox in the Checked column to the left of each row to export.
  20. For information, see Check items on the pages of a result file.
  21. In the Options area of the dialog box, select the Excluded Items Only checkbox.
  22. Otherwise, the application exports all data on the pages that you selected.
  23. If you want the Excel workbook to automatically open after the application finishes exporting the data, select the Open File After Export checkbox.
  24. Select Export, or to cancel this operation and any changes you made, select Close.
  25. If you export the results, a meter appears at the bottom of the Export to Excel dialog box to indicate the progress.
  26. When the export job is complete, select OK in the confirmation box.

If you selected the Open File After Export checkbox in the Export to Excel dialog box, the Excel file automatically opens.

The pages associated with the Level 1 page appear as nested groups in the Excel spreadsheet when you select the plus (+) signs on the left. For example, the three layers (proteins, peptide groups, and PSMs) in appear in the exported Excel file. The following figures show an example.

Export to Excel dialog box set up to export proteins, peptide groups, and PSMs
Export to Excel dialog box set up to export proteins, peptide groups, and PSMs
Three layers shown as associated tables in the exported result file
Three layers shown as nested groups in the exported Excel workbook

The Excel file name is composed of the destination file name and the Level 1 export type, for example, D:\tmp\test_001_Proteins.xlsx.