To export proteins containing crosslinked peptides in search results to xiNET

Procedure

  1. Open your search results in the result file. Refer to “Organizing Reports” in the Proteome Discoverer Help.
  2. Select the Proteins tab.
  3. Select File > Export > To xiNET.
  4. The To xiNET dialog box opens.
  5. In the Destination Folder box, do either of the following:
  6. Enter the path and name of the file where you want to save the exported proteins.
  7. Browse to select the file, and then select Save in the Save As dialog box.
  9. To export only certain crosslinks, do the following:
  10. On the Proteins page of the result file, select the checkbox to the left of each protein group that you want to export. For information on selecting these checkboxes, refer to “Selecting Items on the Pages of the result File” in the Proteome Discoverer Help.
  11. In the To xiNET dialog box, select the Checked Crosslinks Only checkbox.
  12. If you do not select the Checked Proteins Only checkbox, the application exports all protein groups.
  13. (Optional) To automatically access the xiNET website immediately after export so that you can view the resulting CSV file, FASTA file, or both, select the crosslink viewer URL in the To xiNET dialog box.
  14. Do one of the following:
  15. Select Export, and then select OK when the export is finished.
  16. The application exports the selected crosslinks to a CSV file (filename.csv) and a corresponding FASTA file (filename.fasta).

  17. NOTE

    The application does not currently export to Annotation CSV files.

  18. To close the dialog box without exporting any results, select Close.