{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1998","repository_url":"https://api.github.com/repos/OpenMS/OpenMS","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1998/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1998/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1998/events","html_url":"https://github.com/OpenMS/OpenMS/pull/1998","id":156148464,"number":1998,"title":"MultiplexResolver TOPP tool","user":{"login":"lars20070","id":6149805,"avatar_url":"https://avatars.githubusercontent.com/u/6149805?v=3","gravatar_id":"","url":"https://api.github.com/users/lars20070","html_url":"https://github.com/lars20070","followers_url":"https://api.github.com/users/lars20070/followers","following_url":"https://api.github.com/users/lars20070/following{/other_user}","gists_url":"https://api.github.com/users/lars20070/gists{/gist_id}","starred_url":"https://api.github.com/users/lars20070/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lars20070/subscriptions","organizations_url":"https://api.github.com/users/lars20070/orgs","repos_url":"https://api.github.com/users/lars20070/repos","events_url":"https://api.github.com/users/lars20070/events{/privacy}","received_events_url":"https://api.github.com/users/lars20070/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-05-22T11:51:32Z","updated_at":"2016-05-22T13:10:54Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/OpenMS/OpenMS/pulls/1998","html_url":"https://github.com/OpenMS/OpenMS/pull/1998","diff_url":"https://github.com/OpenMS/OpenMS/pull/1998.diff","patch_url":"https://github.com/OpenMS/OpenMS/pull/1998.patch"},"body":"The new `MultiplexResolver` tool removes consensus features in which quantifications and annotated sequences are in conflict. Incomplete multiplets are then completed with zero-intensity dummy features. Resolves #1441. The following three examples from a triple SILAC dataset demonstrate the behaviour of the new tool.\r\n\r\n(1) A sequence with a `Lys8` label was mapped to the heavy peptide of a triplet. The tool passes this consensus feature unchanged to the output.\r\n```\r\n\t\t<consensusElement id=\"e_11446944296506184573\" quality=\"1\" charge=\"2\">\r\n\t\t\t<centroid rt=\"3922.58429977737\" mz=\"937.497195150043\" it=\"6.37687e+08\"/>\r\n\t\t\t<groupedElementList>\r\n\t\t\t\t<element map=\"0\" id=\"0\" rt=\"3922.58429977737\" mz=\"937.497195150043\" it=\"8.27619e+08\" charge=\"2\"/>\r\n\t\t\t\t<element map=\"1\" id=\"0\" rt=\"3922.23240325221\" mz=\"939.509924846113\" it=\"5.47942e+08\" charge=\"2\"/>\r\n\t\t\t\t<element map=\"2\" id=\"0\" rt=\"3922.44347574301\" mz=\"941.503835018594\" it=\"5.37499e+08\" charge=\"2\"/>\r\n\t\t\t</groupedElementList>\r\n\t\t\t<PeptideIdentification identification_run_ref=\"PI_0\" score_type=\"q-value\" higher_score_better=\"false\" significance_threshold=\"0\" MZ=\"941.503845214844\" RT=\"3916.74755859375\" >\r\n\t\t\t\t<PeptideHit score=\"0\" sequence=\"LASVLNTDPALDSELTSK(Label:13C(6)15N(2))\" charge=\"2\" aa_before=\"R\" aa_after=\"L\" protein_refs=\"PH_783\">\r\n\t\t\t\t\t<UserParam type=\"string\" name=\"target_decoy\" value=\"target\"/>\r\n\t\t\t\t\t<UserParam type=\"float\" name=\"consensus_support\" value=\"0\"/>\r\n\t\t\t\t\t<UserParam type=\"string\" name=\"protein_references\" value=\"unique\"/>\r\n\t\t\t\t\t<UserParam type=\"float\" name=\"Posterior Error Probability_score\" value=\"0.0122011053394831\"/>\r\n\t\t\t\t</PeptideHit>\r\n\t\t\t\t<UserParam type=\"int\" name=\"map index\" value=\"2\"/>\r\n\t\t\t</PeptideIdentification>\r\n\t\t</consensusElement>\r\n```\r\n\r\n(2) A sequence with a `Lys8` label was mapped to the light peptide of a triplet. ID and quantification are in conflict. The tool removes this consensus feature from the output.\r\n```\r\n\t\t<consensusElement id=\"e_5220748901194703231\" quality=\"1\" charge=\"2\">\r\n\t\t\t<centroid rt=\"3927.74344766135\" mz=\"757.401025658071\" it=\"1.11311e+08\"/>\r\n\t\t\t<groupedElementList>\r\n\t\t\t\t<element map=\"0\" id=\"0\" rt=\"3927.74344766135\" mz=\"757.401025658071\" it=\"1.56924e+08\" charge=\"2\"/>\r\n\t\t\t\t<element map=\"1\" id=\"0\" rt=\"3924.13450423038\" mz=\"760.411176766411\" it=\"9.60531e+07\" charge=\"2\"/>\r\n\t\t\t\t<element map=\"2\" id=\"0\" rt=\"3922.72834795447\" mz=\"762.405476274356\" it=\"8.09567e+07\" charge=\"2\"/>\r\n\t\t\t</groupedElementList>\r\n\t\t\t<PeptideIdentification identification_run_ref=\"PI_0\" score_type=\"q-value\" higher_score_better=\"false\" significance_threshold=\"0\" MZ=\"757.401000976563\" RT=\"3923.15502929688\" >\r\n\t\t\t\t<PeptideHit score=\"0.00259571706683971\" sequence=\"LINIDFTDPDESK(Label:13C(6)15N(2))\" charge=\"2\" aa_before=\"R\" aa_after=\"W\" protein_refs=\"PH_709\">\r\n\t\t\t\t\t<UserParam type=\"string\" name=\"target_decoy\" value=\"target\"/>\r\n\t\t\t\t\t<UserParam type=\"float\" name=\"consensus_support\" value=\"0\"/>\r\n\t\t\t\t\t<UserParam type=\"string\" name=\"protein_references\" value=\"unique\"/>\r\n\t\t\t\t\t<UserParam type=\"float\" name=\"Posterior Error Probability_score\" value=\"0.128303432755731\"/>\r\n\t\t\t\t</PeptideHit>\r\n\t\t\t\t<UserParam type=\"int\" name=\"map index\" value=\"0\"/>\r\n\t\t\t</PeptideIdentification>\r\n\t\t</consensusElement>\r\n```\r\n\r\n(3) A sequence with a `Lys8` label was mapped to the heavy peptide of a doublet. One feature is missing from the triplet.\r\n```\r\n\t\t<consensusElement id=\"e_7194948732119327551\" quality=\"1\" charge=\"2\">\r\n\t\t\t<centroid rt=\"3918.80712435544\" mz=\"695.885183639542\" it=\"8.84704e+07\"/>\r\n\t\t\t<groupedElementList>\r\n\t\t\t\t<element map=\"0\" id=\"0\" rt=\"3918.80712435544\" mz=\"695.885183639542\" it=\"8.33999e+07\" charge=\"2\"/>\r\n\t\t\t\t<element map=\"1\" id=\"0\" rt=\"3919.30314514029\" mz=\"697.880398564538\" it=\"9.35409e+07\" charge=\"2\"/>\r\n\t\t\t</groupedElementList>\r\n\t\t\t<PeptideIdentification identification_run_ref=\"PI_0\" score_type=\"q-value\" higher_score_better=\"false\" significance_threshold=\"0\" MZ=\"697.88037109375\" RT=\"3917.83227539063\" >\r\n\t\t\t\t<PeptideHit score=\"0.00259571706683971\" sequence=\"LEIC(Carbamidomethyl)NLTPDALK(Label:13C(6)15N(2))\" charge=\"2\" aa_before=\"K\" aa_after=\"S\" protein_refs=\"PH_1268\">\r\n\t\t\t\t\t<UserParam type=\"string\" name=\"target_decoy\" value=\"target\"/>\r\n\t\t\t\t\t<UserParam type=\"float\" name=\"consensus_support\" value=\"0\"/>\r\n\t\t\t\t\t<UserParam type=\"string\" name=\"protein_references\" value=\"unique\"/>\r\n\t\t\t\t\t<UserParam type=\"float\" name=\"Posterior Error Probability_score\" value=\"0.121271304168165\"/>\r\n\t\t\t\t</PeptideHit>\r\n\t\t\t\t<UserParam type=\"int\" name=\"map index\" value=\"1\"/>\r\n\t\t\t</PeptideIdentification>\r\n\t\t</consensusElement>\r\n```\r\nThe tool adds a dummy peptide feature of zero intensity at the light position and thereby completes the triplet.\r\n```\r\n\t\t<consensusElement id=\"e_15157403601844400700\" quality=\"1\" charge=\"2\">\r\n\t\t\t<centroid rt=\"3918.80712435544\" mz=\"693.872630147742\" it=\"8.84704e+07\"/>\r\n\t\t\t<groupedElementList>\r\n\t\t\t\t<element map=\"0\" id=\"0\" rt=\"3918.80712435544\" mz=\"693.872630147742\" it=\"0\" charge=\"2\"/>\r\n\t\t\t\t<element map=\"1\" id=\"0\" rt=\"3918.80712435544\" mz=\"695.885183639542\" it=\"8.33999e+07\" charge=\"2\"/>\r\n\t\t\t\t<element map=\"2\" id=\"0\" rt=\"3919.30314514029\" mz=\"697.880398564538\" it=\"9.35409e+07\" charge=\"2\"/>\r\n\t\t\t</groupedElementList>\r\n\t\t\t<PeptideIdentification identification_run_ref=\"PI_0\" score_type=\"q-value\" higher_score_better=\"false\" significance_threshold=\"0\" MZ=\"697.88037109375\" RT=\"3917.83227539063\" >\r\n\t\t\t\t<PeptideHit score=\"0.00259571706683971\" sequence=\"LEIC(Carbamidomethyl)NLTPDALK(Label:13C(6)15N(2))\" charge=\"2\" aa_before=\"K\" aa_after=\"S\" protein_refs=\"PH_1268\">\r\n\t\t\t\t\t<UserParam type=\"string\" name=\"target_decoy\" value=\"target\"/>\r\n\t\t\t\t\t<UserParam type=\"float\" name=\"consensus_support\" value=\"0\"/>\r\n\t\t\t\t\t<UserParam type=\"string\" name=\"protein_references\" value=\"unique\"/>\r\n\t\t\t\t\t<UserParam type=\"float\" name=\"Posterior Error Probability_score\" value=\"0.121271304168165\"/>\r\n\t\t\t\t</PeptideHit>\r\n\t\t\t\t<UserParam type=\"int\" name=\"map index\" value=\"2\"/>\r\n\t\t\t</PeptideIdentification>\r\n\t\t</consensusElement>\r\n```"},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/220831637","html_url":"https://github.com/OpenMS/OpenMS/pull/1998#issuecomment-220831637","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1998","id":220831637,"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},"created_at":"2016-05-22T13:10:54Z","updated_at":"2016-05-22T13:10:54Z","body":"Hi @lars20070 \r\n\"(2) A sequence with a Lys8 label was mapped to the light peptide of a triplet. ID and quantification are in conflict. The tool removes this consensus feature from the output.\"\r\nWould it be more flexible to remove the annotation instead of the cfeature?"}}
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