Ambiguity
As with any proteomics search algorithm, ambiguities will arise for matches to certain MS2 scans.
The default setting in MetaMorpheus is to report all legal peptides that tie for the highest score, and then report all possible proteins from which those peptides may have originated.
Another option is to report only a single peptide in the event of a tie (random as to which one gets listed), and then include all possible proteins from which that peptide may have originated. (To choose this option for your search: unselect the checkbox named "Report PSM Ambiguity" which can be found in SearchTask -> Search Parameters -> Ambiguity Parameters.)
A third possibility, which is not currently implemented in MetaMorpheus but could be in a future version, is to report all peptide matches independent of score. This would be any peptide within the parent mass tolerance, regardless of the number of matching fragments.
MetaMorpheus psmtsv results have a column with the header "Ambiguity Level". This column contains an ambiguity level for each identification, as defined by Smith et al. This classification was originally designed for proteoform identifications, but is equally effective at communicating ambiguity in peptide identifications. A description for each ambiguity level is available below:
