Ambiguity

There are four levels of ambiguity available for matches to an MS2 scan. Level 2 is default and Level 3 is optional. Levels 1 and 4 are not currently implemented but may be in a future version.

Level 1: Report all legal peptide matches. This would be any peptide within the parent mass tolerance, regardless of the number of matching fragments. Level 2: Report all legal peptides with that have the same score (fragment matching count and total matching intensity). Level 3: Report single compact peptide (considers only a series of fragment ions dissociated from sequence) with possibly many sequences and accessions. Level 4: Report a single match chosen at random from the list of equivalent top-scoring matches.