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,

• masked protein groups will be identified in navigation (see context protein groups).
• in peptides list, peptides referenced by only hidden protein groups will be identified in the same way.

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 impacted and (even if not necessary), they could be applied to all protein groups.

If user choose to apply filter on individual proteins, valid protein groups may contains valid and masked proteins.

In visualization, the protein group view identify masked proteins in sameset and/or subset lists.

For the export :

• only valid (none masked) protein are considered when exporting to AMT db.
• for reports, only one report is impacted (same subset detail report) and for each protein in valid protein groups, the masked property is indicated.

• The Contexts comparison algorithm is impacted in the same way as when protein groups are masked : only valid proteins should be considered.
• Change typical protein operation does not select masked protein as typical !

The other algorithms (spectral count / grouping (peptide to consider) are not impacted.