{"action":"created","issue":{"url":"https://api.github.com/repos/HUPO-PSI/mzTab/issues/26","repository_url":"https://api.github.com/repos/HUPO-PSI/mzTab","labels_url":"https://api.github.com/repos/HUPO-PSI/mzTab/issues/26/labels{/name}","comments_url":"https://api.github.com/repos/HUPO-PSI/mzTab/issues/26/comments","events_url":"https://api.github.com/repos/HUPO-PSI/mzTab/issues/26/events","html_url":"https://github.com/HUPO-PSI/mzTab/issues/26","id":224723715,"number":26,"title":"Assays of fractionated data needs rework.","user":{"login":"timosachsenberg","id":5803621,"avatar_url":"https://avatars3.githubusercontent.com/u/5803621?v=4","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,"assignees":[],"milestone":null,"comments":10,"created_at":"2017-04-27T09:23:29Z","updated_at":"2017-08-09T08:16:40Z","closed_at":null,"body":"One assay is reported for all fractions. This does not allow to model fractionated design with channel swaps between fractions (though I don't know how relevant this is).\r\nExample: consider Assay 1 (A1). It is bound to one channel (e.g., 114 of an iTRAQ experiment)\r\nA1 iTRAQ reagent 114\r\n\r\nAt the same time it is bound to 3 ms_runs (one for each fraction) \r\nA1 F1,F2,F3\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/HUPO-PSI/mzTab/issues/comments/321186749","html_url":"https://github.com/HUPO-PSI/mzTab/issues/26#issuecomment-321186749","issue_url":"https://api.github.com/repos/HUPO-PSI/mzTab/issues/26","id":321186749,"user":{"login":"andrewrobertjones","id":16800053,"avatar_url":"https://avatars3.githubusercontent.com/u/16800053?v=4","gravatar_id":"","url":"https://api.github.com/users/andrewrobertjones","html_url":"https://github.com/andrewrobertjones","followers_url":"https://api.github.com/users/andrewrobertjones/followers","following_url":"https://api.github.com/users/andrewrobertjones/following{/other_user}","gists_url":"https://api.github.com/users/andrewrobertjones/gists{/gist_id}","starred_url":"https://api.github.com/users/andrewrobertjones/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrewrobertjones/subscriptions","organizations_url":"https://api.github.com/users/andrewrobertjones/orgs","repos_url":"https://api.github.com/users/andrewrobertjones/repos","events_url":"https://api.github.com/users/andrewrobertjones/events{/privacy}","received_events_url":"https://api.github.com/users/andrewrobertjones/received_events","type":"User","site_admin":false},"created_at":"2017-08-09T08:16:40Z","updated_at":"2017-08-09T08:16:40Z","body":"Yes on balance my suggestion does seem over-complicated. I was thinking there could be cases where the data had not been aligned with missing features etc, but in that case it could still be linked via your mechanism. I would favour this kind of encoding for the fractions:\r\n\r\n`MTD ms_run[1-n]-fraction[1-n]-location LOCATIONOFRAWFILE.raw`\r\n\r\nThe using this kind of encoding at the peptide level:\r\n\r\n`PEH sequence ... cv_opt_global_ms_runs \r\nPEP VLPASLAANIPVK ... 1.6; 2.6; 3.6\r\nPEP VLPASLAANIPVK ... 1.7;  2.7; 3:7...\r\n`\r\nSo that fractions always stay obviously linked to ms_runs.\r\n\r\n\r\n"}}
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