Alternately, you can also run ProteinProphet separately and load the data manually into CPAS. If you have ProteinProphet data that you want to load into CPAS, make sure that your folder has a data pipeline configured to point to the right directory on your file system. On the Pipeline tab, click the Process and Upload Data button and browsing to the directory containing your ProteinProphet results. CPAS recognizes .prot.xml and .pep-prot.xml files as ProteinProphet data. Click on the corresponding Import ProteinProphet button. CPAS will load the MS2 run from the .pep.xml file, if needed, and associate the ProteinProphet data with it.

To view the data, navigate to the MS2 run in CPAS. Assuming the data imported correctly, there will be two new grouping options – Protein Prophet Collapsed and Protein Prophet Expanded. Select one of them to see the protein groups, as well as the indistinguishable proteins in the groups. The expanded view will show you all of the peptides assigned to that group, or you can click to expand individual groups in the collapsed view.

There are additional peptide-level and protein-level columns available in the ProteinProphet views. Click on either the Pick Peptide Columns or Pick Protein Columns buttons to view the full list and choose which ones you want to include.