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.

• If protein groups are filtered, the typical protein is considered but the whole group is (eventually) marked as hidden.
• If proteins are filtered, each proteins of each protein groups are considered and (eventually) marked as hidden. If typical protein is set hidden, then another sameset protein is set as typical. If there is no more none hidden sameset then the whole protein group is set as hidden.

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, hidden protein groups will be identified in navigation (context protein groups list).

The export operations will only work on valid (none hidden) protein groups as well as the Contexts comparison algorithm. The other algorithms (change master / spectral count / protein grouping (peptide to consider) should not be impacted and even if not necessary, they could be applied to all protein groups).

[ TODO peptides referenced by (only ?) hidden protein groups should be identified in the same way in peptides list]

Hidden individual protein have more impact as in a valid protein group, only some of the proteins may be valid.

In visualization, the protein group view hidden proteins are identified. The export also have to considerate only none hidden proteins when exporting protein groups details or AMT db. 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).