{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2497","repository_url":"https://api.github.com/repos/OpenMS/OpenMS","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2497/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2497/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2497/events","html_url":"https://github.com/OpenMS/OpenMS/issues/2497","id":219190060,"number":2497,"title":"X!Tandem reporting of non-tryptic peptides not reported/considered","user":{"login":"cbielow","id":6008722,"avatar_url":"https://avatars0.githubusercontent.com/u/6008722?v=4","gravatar_id":"","url":"https://api.github.com/users/cbielow","html_url":"https://github.com/cbielow","followers_url":"https://api.github.com/users/cbielow/followers","following_url":"https://api.github.com/users/cbielow/following{/other_user}","gists_url":"https://api.github.com/users/cbielow/gists{/gist_id}","starred_url":"https://api.github.com/users/cbielow/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cbielow/subscriptions","organizations_url":"https://api.github.com/users/cbielow/orgs","repos_url":"https://api.github.com/users/cbielow/repos","events_url":"https://api.github.com/users/cbielow/events{/privacy}","received_events_url":"https://api.github.com/users/cbielow/received_events","type":"User","site_admin":false},"labels":[{"id":74106698,"url":"https://api.github.com/repos/OpenMS/OpenMS/labels/blocker","name":"blocker","color":"e11d21","default":false},{"id":74106459,"url":"https://api.github.com/repos/OpenMS/OpenMS/labels/defect","name":"defect","color":"f7c6c7","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/OpenMS/OpenMS/milestones/11","html_url":"https://github.com/OpenMS/OpenMS/milestone/11","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/milestones/11/labels","id":2228556,"number":11,"title":"Release 2.2","description":"","creator":{"login":"okohlbacher","id":1107303,"avatar_url":"https://avatars1.githubusercontent.com/u/1107303?v=4","gravatar_id":"","url":"https://api.github.com/users/okohlbacher","html_url":"https://github.com/okohlbacher","followers_url":"https://api.github.com/users/okohlbacher/followers","following_url":"https://api.github.com/users/okohlbacher/following{/other_user}","gists_url":"https://api.github.com/users/okohlbacher/gists{/gist_id}","starred_url":"https://api.github.com/users/okohlbacher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/okohlbacher/subscriptions","organizations_url":"https://api.github.com/users/okohlbacher/orgs","repos_url":"https://api.github.com/users/okohlbacher/repos","events_url":"https://api.github.com/users/okohlbacher/events{/privacy}","received_events_url":"https://api.github.com/users/okohlbacher/received_events","type":"User","site_admin":false},"open_issues":11,"closed_issues":39,"state":"open","created_at":"2017-01-04T16:45:31Z","updated_at":"2017-09-28T07:54:46Z","due_on":"2017-06-27T07:00:00Z","closed_at":null},"comments":17,"created_at":"2017-04-04T09:27:24Z","updated_at":"2017-12-01T10:07:05Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Running X!Tandem (Vengeane 2015.12.15.2) in KNIME using `Trypsin` as enzyme yields peptides such as\r\n`AKIDELINND`, which is clearly not tryptic on either C or N Terminus.\r\nThe N-Terminus I can understand somewhat, but why is 'D' (aspartate) considered a valid cutting site?\r\nThe protein is here:\r\n```\r\n>sp|Q12051|GGPPS_YEAST .... GN=BTS1 PE=1 SV=1\r\nME*AKIDELINND*PVWSSQNE....\r\n```\r\n\r\nI've searched for an explanation, and found `[X]|[D]` in the Tandem docs (http://www.thegpm.org/TANDEM/api/pcs.html) as possible cutting rule (aspn), but thats the N-terminal, not C-terminal and even checking the default.xml seems to specifiy Trypsin only.\r\n\r\nSo why does XTandem report these peptides? This has implications for PeptideIndexing, but if we dont understand the reasons, its hard to model why this should be allowed."},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/348454747","html_url":"https://github.com/OpenMS/OpenMS/issues/2497#issuecomment-348454747","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/2497","id":348454747,"user":{"login":"jpfeuffer","id":8102638,"avatar_url":"https://avatars0.githubusercontent.com/u/8102638?v=4","gravatar_id":"","url":"https://api.github.com/users/jpfeuffer","html_url":"https://github.com/jpfeuffer","followers_url":"https://api.github.com/users/jpfeuffer/followers","following_url":"https://api.github.com/users/jpfeuffer/following{/other_user}","gists_url":"https://api.github.com/users/jpfeuffer/gists{/gist_id}","starred_url":"https://api.github.com/users/jpfeuffer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jpfeuffer/subscriptions","organizations_url":"https://api.github.com/users/jpfeuffer/orgs","repos_url":"https://api.github.com/users/jpfeuffer/repos","events_url":"https://api.github.com/users/jpfeuffer/events{/privacy}","received_events_url":"https://api.github.com/users/jpfeuffer/received_events","type":"User","site_admin":false},"created_at":"2017-12-01T10:07:05Z","updated_at":"2017-12-01T10:07:05Z","author_association":"CONTRIBUTOR","body":"I'm working on it."}}
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