Hi Anna,
You could use File > Share - Minimal to save your documents in a way that their libraries only contain spectra for the peptides they target. Then when you combine the documents, presumably, you would not see any cases where stray peptide spectrum matches from one library match to peptides in the wrong document. That is if you have documents.
A. with target peptide: APEPTIDER and library A containing spectra matching APEPTIDER AND CPEPTIDER
B. with target peptide: CPEPTIDER and library B containing spectra matching APEPTIDER AND CPEPTIDER
Then simply combining them will have the problem you highlight, where the combined document will use spectra for both target peptides from library A. However, if you first File > Share - Minimized, then you will end up with:
A. with target peptide: APEPTIDER and library A containing spectra matching APEPTIDER
B. with target peptide: CPEPTIDER and library B containing spectra matching CPEPTIDER
And combining them will no longer have this issue.
Would that work for you? If not, please explain. Thanks for posting your issue to the support board.
--Brendan |