Comet parameter: peff_format

• Specifies whether the database is a PEFF file or normal FASTA.
• Valid values are 0, 1, 2, 3, 4, 5.
• Set this parameter to 0 to search a normal FASTA file, ignoring any PEFF annotations if present.
• Set this parameter to 1 to search PEFF PSI-MOD modifications and amino acid variants.
• Set this parameter to 2 to search PEFF Unimod modifications and amino acid variants.
• Set this parameter to 3 to search PEFF PSI-MOD modifications, skipping amino acid variants.
• Set this parameter to 4 to search PEFF Unimod modifications, skipping amino acid variants.
• Set this parameter to 5 to search PEFF amino acid variants, skipping PEFF modifications.
• The default value is “0” if this parameter is missing.
• Modifications are read from the “\ModResPsi” (values 1 and 3) or “\ModResUnimod” (values 2 and 4) header attributes, with masses looked up in the peff_obo file. Amino acid variants are read from the “\VariantSimple” and “\VariantComplex” attributes (values 1, 2 and 5).
• peff_obo must be set for any non-zero value, including 5.
• Each peptide is analyzed with at most one PEFF modification or one PEFF amino acid variant, never both and never two of either. A PEFF modification can be combined with regular variable modifications on other residues and does not count toward max_variable_mods_in_peptide.
• PEFF annotations are applied only when searching the PEFF file itself, which is always a regular (non-indexed) search regardless of the index_search_type setting. They are not carried into an indexed database (.idx file) built from the PEFF file.
• Release 2026.03.0 fixes these PEFF header parsing issues:
  • Annotation identifiers (“# HasAnnotationIdentifiers=true”, e.g. “\ModResPsi=(1:25|MOD:00798|half cystine)”) are now handled correctly; earlier releases read the label as the position, so labeled modifications were placed on the wrong residue and labeled variants were dropped.
  • Modification names containing parentheses (e.g. “N6-(4-amino-2-hydroxybutyl)-L-lysine”) no longer cause entries to be misread or dropped.
  • A “\VariantSimple” entry with an empty residue field is now ignored instead of being searched as a variant with the previous entry’s residue.
• Set peff_verbose_output to 1 to report annotation entries that are ignored.

Example:

peff_format = 0
peff_format = 1
peff_format = 5