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
- From the Proteome Discoverer Start Page, open the bottom-up result that you want to create a top-down database from.
- Select File > Export > To mzIdentML.
- The Export to mzIdentML dialog box opens.
- Select Browse and locate the Destination Folder.
- Select Export.
- 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.
- The ProSightPD Database Manager opens.
- Select Create ProSightPD Database.
- Select Browse.
- The Open dialog box opens.
- In the file type box at the bottom right corner, select MzIdentML (*.mzid file) as shown in the following figure.
- Select the exported results and select Open.
- Create and save a top-down database using the ProSightPD Database Manager tool. See Create a database in ProSightPD for more information.