Anette,
It sounds like you were taking the right actions. by defining the views at the project level.
But just to make sure you are clear on the views involved: There are really two filtered views that need to be there for your scenarios, and their names need to match.
When you click on a run to go to run details, the data set you see is the Peptides query, and the view you define here affects the peptide grid on that run details page and the matching peptides grid at the bottom of the protein details page.
On the Compare peptides setup page, the view you are defining there is on the hidden PeptidesFilter query. To keep this view consistent with the Peptides view described above, it should have the same filter terms and be saved under the same name (lower case/upper case matters) as the view on the Peptides query.
I suspect you already knew the above. Perhaps you should try a test by saving the views under a new name at the project level, as a test. Then see if both views are available as expected in a subfolder. |