Peptides appear greyed out in the Peptide Alternatives view due to the applied filtering settings. In the example shown in Figure 1, only sequence variants are selected in the Peptide Type filter (see Figure 2). Since the greyed-out peptide is not a sequence variant, it is displayed as an alternative but cannot be selected for replacement.
To enable replacement functionality for this peptide, its type must also be included in the Peptide Type filter. Once the appropriate type is selected, the peptide is no longer greyed out and can be used to replace the current peptide (see Figure 3).
Figure 1. Greyed out peptide alternatives
Figure 2. Peptide type filters within the search filters.
Figure3. Peptide alternative view after removing the peptide type filter.