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On a User Context it is possible to apply filters. Filter will mark as hidden (or masked) protein groups or proteins inside protein groups (depending on user choice) which respect user defined criteria.
The available filters are described in the how to filter proteins [groups] .
Once protein or proteins groups are marked as masked, they will be taken into account is some operations.
In visualization,
The export operations (for AMT or reports) will only export valid (none masked) protein groups. This is also the case for Contexts comparison
algorithm.
The other algorithms (change master / spectral count / protein grouping (peptide to consider) are not be impacted and (even if not necessary), they could be applied to all protein groups.
If user choose to apply filter on individual masked proteins, valid protein groups may contains valid and masked proteins.
In visualization, the protein group view identify hidden proteins in sameset and/or subset lists.
For the export :
The contexts comparison algorithm is impacted in the same way as when protein groups are masked : only valid protein should be considered. In the same way, change typical protein does not select hidden protein as typical ! The other algorothms (spectral count / grouping (peptide to consider) should not be impacted).