{"action":"created","comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/comments/51713074","id":51713074,"diff_hunk":"@@ -327,12 +329,29 @@ class TOPPIDFileConverter :\n           MascotXMLFile::initializeLookup(lookup, exp, scan_regex);\n           PepXMLFile().load(in, protein_identifications,\n                             peptide_identifications, exp_name, lookup);\n+          bool reset_basename = getFlag_(\"reset_basename\");\n+          bool add_ions = getFlag_(\"add_ionmatch_annotation\");\n+          if (add_ions)\n+          {\n+            SpectrumMetaDataLookup::addMissingSpectrumReferencestoPeptideIDs(\n+                      peptide_identifications, exp_name, false, add_ions, reset_basename);\n+          }","path":"src/topp/IDFileConverter.cpp","position":19,"original_position":19,"commit_id":"6dd94cdd439a3ee0493a64b402ab13dd96d94c35","original_commit_id":"6dd94cdd439a3ee0493a64b402ab13dd96d94c35","user":{"login":"timosachsenberg","id":5803621,"avatar_url":"https://avatars.githubusercontent.com/u/5803621?v=3","gravatar_id":"","url":"https://api.github.com/users/timosachsenberg","html_url":"https://github.com/timosachsenberg","followers_url":"https://api.github.com/users/timosachsenberg/followers","following_url":"https://api.github.com/users/timosachsenberg/following{/other_user}","gists_url":"https://api.github.com/users/timosachsenberg/gists{/gist_id}","starred_url":"https://api.github.com/users/timosachsenberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timosachsenberg/subscriptions","organizations_url":"https://api.github.com/users/timosachsenberg/orgs","repos_url":"https://api.github.com/users/timosachsenberg/repos","events_url":"https://api.github.com/users/timosachsenberg/events{/privacy}","received_events_url":"https://api.github.com/users/timosachsenberg/received_events","type":"User","site_admin":false},"body":"reannotation without knowing details on fragmentation method / tolerances does make very litte sense. Here you would have this information available and could call e.g. a method from a not-ecisting SpectrumReannotation 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