{"action":"created","issue":{"url":"https://api.github.com/repos/compomics/searchgui/issues/72","labels_url":"https://api.github.com/repos/compomics/searchgui/issues/72/labels{/name}","comments_url":"https://api.github.com/repos/compomics/searchgui/issues/72/comments","events_url":"https://api.github.com/repos/compomics/searchgui/issues/72/events","html_url":"https://github.com/compomics/searchgui/issues/72","id":123598524,"number":72,"title":"X!Tandem parameter file: variable N-terminal modifications","user":{"login":"ulriche","id":13509447,"avatar_url":"https://avatars.githubusercontent.com/u/13509447?v=3","gravatar_id":"","url":"https://api.github.com/users/ulriche","html_url":"https://github.com/ulriche","followers_url":"https://api.github.com/users/ulriche/followers","following_url":"https://api.github.com/users/ulriche/following{/other_user}","gists_url":"https://api.github.com/users/ulriche/gists{/gist_id}","starred_url":"https://api.github.com/users/ulriche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ulriche/subscriptions","organizations_url":"https://api.github.com/users/ulriche/orgs","repos_url":"https://api.github.com/users/ulriche/repos","events_url":"https://api.github.com/users/ulriche/events{/privacy}","received_events_url":"https://api.github.com/users/ulriche/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/compomics/searchgui/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":{"login":"mvaudel","id":11632644,"avatar_url":"https://avatars.githubusercontent.com/u/11632644?v=3","gravatar_id":"","url":"https://api.github.com/users/mvaudel","html_url":"https://github.com/mvaudel","followers_url":"https://api.github.com/users/mvaudel/followers","following_url":"https://api.github.com/users/mvaudel/following{/other_user}","gists_url":"https://api.github.com/users/mvaudel/gists{/gist_id}","starred_url":"https://api.github.com/users/mvaudel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvaudel/subscriptions","organizations_url":"https://api.github.com/users/mvaudel/orgs","repos_url":"https://api.github.com/users/mvaudel/repos","events_url":"https://api.github.com/users/mvaudel/events{/privacy}","received_events_url":"https://api.github.com/users/mvaudel/received_events","type":"User","site_admin":false},"milestone":null,"comments":4,"created_at":"2015-12-23T03:57:42Z","updated_at":"2016-01-15T04:02:25Z","closed_at":null,"body":"Hey folks,\r\n\r\nnot sure as no results yet, but I am a bit confused about the X!Tandem parameter file - but it may be right (couldn't check anymore as I have to leave the lab now and fly to Europe tomorrow).\r\n\r\nThat are my SearchGUI settings:\r\n![image](https://cloud.githubusercontent.com/assets/13509447/11970691/6fb533ec-a8e4-11e5-9223-f8803ca508a3.png)\r\n\r\nwhy does it translate to:\r\n![image](https://cloud.githubusercontent.com/assets/13509447/11970713/bfd682a4-a8e4-11e5-8064-35bdd6973be3.png)\r\n\r\n-> I understand the first three, so fixed cmCys & TMT6@K, and variable Met-Ox.\r\n\r\nbut I don't understand the variable N-terminal ones. i guess the pyro-ones are handled by the quick-pyrolidone function, but what happens to the N-terminal acetyl and TMT? why do they end up in the \"potential modification motif\"? (on a sidenote, the quick acetyl option in X! Tandem only works for something like the first 50 aminoacids in a protein (but don't know the exact number), and is thus not sufficient in our cases. any idea?\r\n\r\nall the best\r\nu"},"comment":{"url":"https://api.github.com/repos/compomics/searchgui/issues/comments/171866714","html_url":"https://github.com/compomics/searchgui/issues/72#issuecomment-171866714","issue_url":"https://api.github.com/repos/compomics/searchgui/issues/72","id":171866714,"user":{"login":"ulriche","id":13509447,"avatar_url":"https://avatars.githubusercontent.com/u/13509447?v=3","gravatar_id":"","url":"https://api.github.com/users/ulriche","html_url":"https://github.com/ulriche","followers_url":"https://api.github.com/users/ulriche/followers","following_url":"https://api.github.com/users/ulriche/following{/other_user}","gists_url":"https://api.github.com/users/ulriche/gists{/gist_id}","starred_url":"https://api.github.com/users/ulriche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ulriche/subscriptions","organizations_url":"https://api.github.com/users/ulriche/orgs","repos_url":"https://api.github.com/users/ulriche/repos","events_url":"https://api.github.com/users/ulriche/events{/privacy}","received_events_url":"https://api.github.com/users/ulriche/received_events","type":"User","site_admin":false},"created_at":"2016-01-15T04:02:25Z","updated_at":"2016-01-15T04:02:25Z","body":"any updates/ideas on that? haven't checked with the updated SearchGUI though."}}