PEFF Distinguish SAAV and PTM

[OK]

How does Comet distinguish between SAAV's with close mass offsets (ex. D to N) and/or between SAAV's and common PTMs with similar mass offsets when doing a PEFF search? 

Is there anything we can do to distinguish these?

[Jimmy Eng]

Comet doesn't do anything beyond scoring the various peptides that fall within the precursor tolerances.  And distinguishing between a SAAV that substitutes a D to N is no different than distinguishing between those two peptides forms being present in a regular FASTA.  The criteria Comet uses to rank/score peptides is the cross correlation score and there's no other secondary or special scoring function available (whether specifically for peptides with close mass offsets or all candidate peptides in general).  Note that a SAAV with a D to N substitution would shift half of all of the theoretical fragment ions by ~1 Da so that should impart a pretty significant impact on the spectral score comparison.

Depending on how many spectra you need to distinguish, I might manually inspect the spectra against both peptide forms.  Or use another tool, such as Mascot/MSFragger/Sage which all use a different score function (hyperscore) to score the spectra against a database containing both peptide forms.