Here's some notes on Comet's internally-generated decoy peptides.

• A decoy peptide is generated for each target peptide scored. This guarantees a 1:1 ratio of target to decoy peptides.
• Decoy peptides keeps a terminal residue fixed (e.g. the last K or R for a tryptic peptide) and reverses every other residue in the peptide. For an enzyme that cleaves n-terminal to a residue, such as AspN, the first residue in the peptide is fixed and every other residue is reversed. For example, target tryptic peptide CLSTWGK will generate a decoy peptide GWTSLCK. A target AspN peptide DSANLPQ will generate a decoy peptide DQPLNAS.
• If a residue is modified, the modification will move with the residue in the decoy peptide e.g. M[15.9949]QEATLSK will generate a decoy peptide SLTAEQM[15.9949]K. If there were a distance constraint forcing this modification to only appear on the n-terminal residue of the peptide, this constraint is not enforced for the decoys.