handle percolator pin file generated by comet

Author: ATPs

psm_utils/io/percolator.py

@@ -149,9 +149,15 @@ def _infer_charge_columns(fieldnames):
     @staticmethod
     def _parse_peptidoform(percolator_peptide, charge):
         """Parse Percolator TSV peptide notation to Peptidoform."""
-        # Remove leading and trailing amino acids
+        # Remove leading and trailing amino acids (e.g., R.PEPTIDE.S -> PEPTIDE)
         match = re.match(r"^(?:[A-Z-])?\.(.+)\.(?:[A-Z-])?$", percolator_peptide)
         peptidoform = match[1] if match else percolator_peptide
+        # Handle Comet's n-terminal modification format: n[42.0106]PEPTIDE
+        peptidoform = re.sub(r'^n\[([+-]?[\w\.]*?)\]', r'[\1]-', peptidoform)
+        
+        # Ensure positive values inside square brackets have a '+' sign
+        peptidoform = re.sub(r'\[(\d+[\.]*\d*)]', r'[+\1]', peptidoform)
+        
         if charge:
             peptidoform += f"/{charge}"
         return Peptidoform(peptidoform)