Ambiguity

There are three levels of ambiguity available for matches to an MS2 scan. Level 2 is default and Level 3 is optional. Level 1 is not currently implemented but may be in a future version.

Level 1: Report all peptide matches independent of score. This would be any peptide within the parent mass tolerance, regardless of the number of matching fragments.

Level 2: Report all legal peptides that tie for the highest score. (Default)

Level 3: Report a single peptide in the event of a tie, but includes all possible proteins that peptide may have originated from. (Use this level by unselecting "Report All Ambiguity" in SearchTask -> Search Parameters -> Ambiguity Parameters)