Comet parameter: print_ascorepro_score

• This parameter determines whether or not the AScorePro algorithm is applied to the search results.
• The AScorePro algorithm is only applied to the top ranked hit for each spectrum query.
• If it is applied, the AScorePro MOB score will be available in the real-time search interface as well as .txt, .pep.xml, and .mzid output formats.
• In the .txt output, the AScorePro MOB score is reported in a column titled “ascorepro”.
• In the .pep.xml output, the AScorePro MOB score is reported as a search score using the “ascorepro_score” attribute. The site scores are reported as a search score using the “ascorepro_sitescore” attribute.
• In the .mzid output, the AScorePro MOB score is reported as a search score using the cvParam element with the following attributes: cvRef=”PSI-MS” accession=”MS:1001968” name=”PTM localization PSM-level statistic” value=”X.XXXX”.
• Both the MOB score and site scores are returned through the CometWrapper real-time search interface.
• AScorePro MOB scores are a decimal value whereas site scores are reported as a string composed of space-separated pairs of “position”:”score”. An example site score might be “1:13.86 5:15.94” for the peptide “QAS[79.9663]ES[79.9663]K”.
• When the AScorePro algorithm is applied, any peptide with a MOB score >= 13 will have its localized peptidoform replace Comet’s top ranked peptide. This means that the new top ranked peptidoform might be a duplicate of a lower ranked result.
• Note that the maximum site score is 5000.0 if the variable modification is on the only residue in the peptide that can be modified. Negative and zero site scores are possible; I suggest you contact the AScorePro devs for further details of their algorithm.
• Valid values are
  • “-1” to localize all variable modifications in a peptide
  • “0” to not apply the AScorePro algorithm
  • “1” to localize the modification specified by variable_mod01
  • “2” to localize the modification specified by variable_mod02
  • “3” to localize the modification specified by variable_mod03
  • “4” to localize the modification specified by variable_mod04
  • “5” to localize the modification specified by variable_mod05
  • “6” through “9” to localize the modification specified by variable_mod06 through variable_mod09
• The default value is “0” if this parameter is missing.
• AScorePro localization is supported for variable_mod01 through variable_mod09. Starting with release 2026.03.0, a search that enables this parameter while any of variable_mod10 through variable_mod15 is also set reports an error and does not run.
• Starting with release 2026.03.0, AScorePro honors the distance constraint of a variable modification (fifth and sixth entries, e.g. N-terminal pyroglutamate “-17.026549 Q 0 1 0 2 0 0.0”). A position-restricted modification is never relocalized onto a residue it is not allowed on, and the MOB and site scores are computed among the allowed peptidoforms only.
• Note that this is currently considered an experimental score in Comet. Especially the extension to localize all modifications in a peptide (or any modification that is not phosphorylation per the AScorePro publication). The meaning or utility of the AScorePro MOB score to localize non-phosphorylation modifications will need to be validated.

Example:

print_ascorepro_score = 0     (do not run AScorePro)
print_ascorepro_score = 1     (to localize the variable_mod01 mods)
print_ascorepro_score = 3     (to localize the variable_mod03 mods)
print_ascorepro_score = -1    (to localize all variable mods in a peptide)