{"action":"created","issue":{"url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/13","repository_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML","labels_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/13/comments","events_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/13/events","html_url":"https://github.com/HUPO-PSI/mzIdentML/issues/13","id":151811402,"number":13,"title":"Cross-link site specificity might need refinement","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},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-04-29T07:45:33Z","updated_at":"2016-05-10T12:16:46Z","closed_at":null,"body":"Hi,\r\nI wanted to point out that the current format e.g. \"(K,L,n-term)\" might be insufficient to represent site-specific and site-unspecific terminal cross-linker.\r\ne.g. in unimod there is the distinction between a terminal modification e.g. (\"N-term\") and a terminal modification at a specific site e.g. (\"N-term K\").\r\nMaybe we could also adapt this notation.\r\n"},"comment":{"url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/comments/218140043","html_url":"https://github.com/HUPO-PSI/mzIdentML/issues/13#issuecomment-218140043","issue_url":"https://api.github.com/repos/HUPO-PSI/mzIdentML/issues/13","id":218140043,"user":{"login":"lutzfischer","id":6330440,"avatar_url":"https://avatars.githubusercontent.com/u/6330440?v=3","gravatar_id":"","url":"https://api.github.com/users/lutzfischer","html_url":"https://github.com/lutzfischer","followers_url":"https://api.github.com/users/lutzfischer/followers","following_url":"https://api.github.com/users/lutzfischer/following{/other_user}","gists_url":"https://api.github.com/users/lutzfischer/gists{/gist_id}","starred_url":"https://api.github.com/users/lutzfischer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lutzfischer/subscriptions","organizations_url":"https://api.github.com/users/lutzfischer/orgs","repos_url":"https://api.github.com/users/lutzfischer/repos","events_url":"https://api.github.com/users/lutzfischer/events{/privacy}","received_events_url":"https://api.github.com/users/lutzfischer/received_events","type":"User","site_admin":false},"created_at":"2016-05-10T12:16:46Z","updated_at":"2016-05-10T12:16:46Z","body":"I agree that this would make sense. Hoever at the moment we don't have a cross-linker of type \"N-term K\" or equivalent.\r\nCurrently used are:\r\n* Amino-Acids - signifies that the cross-linker reacts with these amino-acids\r\n* N-term/C-term - refers to N-terminal or C-terminal end of the protein\r\n\r\nIf we want to specify now how things will be treated even if we don't have examples of them then we need a separate document to keep these information.\r\n\r\nOne more related question would be whether it make sense to distinguish protein and peptide terminal. This probably only meaning full if looking at natural occurring cross-links e.g. Ubiguitilation - not sure if there are any natural occurring peptide  C-/N-terminal cross-links.\r\n"}}