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) according user defined criteria.
The available filters are described in the how-to filter proteins [groups] .
If several filters are applied successively, the previous filter(s) is(are) not reset (“cumulative” effect).
Once a protein or a protein groups is masked, it will be taken into account is some operations.
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 :
Contexts comparisonalgorithm is impacted in the same way as when protein groups are masked : only valid proteins should be considered.
Change typical proteinoperation does not select masked protein as typical !
The other algorithms (spectral count / grouping (peptide to consider) are not impacted.