Bottom-up and top-down databases can have complementary applications. One way to leverage both is to combine the depth of protein IDs from bottom-up with the characterization capability of top-down. ProSightPD can utilize the protein ID results (with modifications) from a bottom-up search to create a database for top-down. The steps below describe how to export bottom-up results and create a top-down database.

Procedure

  1. From the Proteome Discoverer Start Page, open the bottom-up result that you want to create a top-down database from.
  2. Select File > Export > To mzIdentML.
  3. The Export to mzIdentML dialog box opens.
  4. Select Browse and locate the Destination Folder.
  5. Select Export.
  6. From the Proteome Discoverer application menu bar, select the ProSightPD Database Manager icon,. See Create a database in ProSightPD for more information on creating databases in ProSightPD.
  7. The ProSightPD Database Manager opens.
  8. Select Create ProSightPD Database.
  9. Select Browse.
  10. The Open dialog box opens.
  11. In the file type box at the bottom right corner, select MzIdentML (*.mzid file) as shown in the following figure.
  12. Select the exported results and select Open.
  13. Create and save a top-down database using the ProSightPD Database Manager tool. See Create a database in ProSightPD for more information.