Anette,

I apologize for the delayed response to your question. In order to do what you ask you will need to use one of LabKey's legacy views. The first step will be to modify the existing view to add in the the DetaCN(DCn) and XCorr columns and then use that view while looking at the proteins in your run. The instructions are below:

1) Start from the dashboard and click on a run.
2) Create a new view
  a) In the webpart named "View", in the Grouping drop down select "Protein (Legacy)" and hit the "go" button next to the drop down
  b) You will now see a new button, in the View webpart, named "Pick Peptide Columns"
  c) Click on the button named "Pick Peptide Columns"
  d) In the text box for the "Current:" field append the following (without the quotes) ',DeltaCN, XCorr'
  f) Click on the "Pick Columns" button
  g) This will bring you back to the previous page
  h) Click on the "Save View" button, in the View webpart, and enter a name of your choosing for this new view.
3) In the View webpart, find the drop down that says " <Select a saved View> " and choose the view that you created in the previous step. Hit the "go" button next to the drop down
4) In the View webpart, in the Grouping drop down, select "Protein (Legacy)". Click on the checkbox for "Expanded" and hit the "go" button next to the drop down.


In the Proteins webpart, you will now see for each Protein found in the run, there is a list of peptides in a table. You should see that DCn and XCorr columns are now in this table(in the last 2 columns). If you click on the column headers in this table, you will notice that you can sort and filter the data using these.

Please note, that you might have a Peptide filter applied to your data which limits the peptides and proteins shown in the view. Any filters or sorts applied to this run, will be shown in the area above the "Proteins" webpart.

Lastly, in step 3 above if you choose

- "Protein (Legacy)" in the drop down, it will display protein information from the search engine
- "ProteinProphet (Legacy)" in the drop down, it will display protein information from the ProteinProphet analysis



* In our next version (11.1) we will be introducing a new workflow to make this much more simple.

Hi Brian,
thanks for your reply.

I went through all the steps mentioned above, but I still don't get the full list of peptides which match this protein. The issue is that I have several other proteins with partially identical sequence in the database. So as soon as one peptide derived from my protein (which I know is the correct hit) is also matching one of those other proteins - this peptide won't show up in the peptide list.

How can I have both: possibility to filter for charge dependent XCorr values and one DCn value and at the same time get the full list of peptides no matter how many other proteins in the database match as well?

Best regards
Anette