Hi Hui,
You might try working backwards by:
- Add everything
- Paste the list of peptides to Excel
- Add a unique by organism constraint
- Paste the list of peptides to Excel
- In Excel use formula like this in column C =IF(COUNTIF(B$1:B$3,A1)>0,A1,"") on the range of unique by organism peptides in column B
- Copy paste the text of column C to a text editor and use Find and Replace to remove the empty rows
- Refine > Accept Peptides and paste your list of non-unique peptides into the form and OK
Something along these lines may get you what you are looking for.
--Brendan