How can I get more identifications using inclusion lists in Progenesis?

An inclusion list can be used to target the collection of MS/MS data from additional LC/MS runs. This is a 2 step process: the first step is to export the inclusion list from Progenesis; the second step is to add the new runs to your existing analysis to associate their ms/ms spectra with the compounds already found by peak picking.

Step 1: Exporting the inclusion list

At the Identify Compounds screen, filter your data to show only those ions for which you wish to collect additional fragmentation data. The quickest way to do is through the use of Quick Tags, specifically the No MS/MS data tag.
To create an inclusion list for these tagged ions, go to File | Export inclusion list… to display the following window:
Select the appropriate instrument type from the inclusion list and then choose where the file should be saved using the Browse button.
Click Export
Note: For Thermo Finnigan inclusion lists you’ll be asked if you want to widen the retention time windows:

Make adjustments as necessary and then click either Yes or No, dependent on whether you wish to widen the retention time windows.
Use the inclusion list(s) to generate additional LC/MS runs, ensuring they are run under the same conditions as the original runs in the analysis.

Step 2: Using the additional runs generated from your inclusion list(s)

Go back to the start of the experiment by selecting Import Data at the top of the screen and import all of the additional runs. After import, click Section Complete.
Run Automatic Alignment for the additional run(s).
Click Section Complete to move to the Experiment Design Setup screen; you can skip over this as there are no changes to be made here.
At Peak Picking, select Start Peak Picking and then, when prompted, click Use existing peak picking.
Click Section Complete to move forward to Review Deconvolution; again, you can skip over this section by clicking Section Complete.

This will bring you to Identify Compounds, where you can use the additional ms/ms spectra to aid your identifications. The ions tagged as having No MS/MS data should now have some associated spectra, dependent on the success of your data collection.