{"action":"closed","issue":{"url":"https://api.github.com/repos/userbz/DeMix/issues/3","repository_url":"https://api.github.com/repos/userbz/DeMix","labels_url":"https://api.github.com/repos/userbz/DeMix/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/userbz/DeMix/issues/3/comments","events_url":"https://api.github.com/repos/userbz/DeMix/issues/3/events","html_url":"https://github.com/userbz/DeMix/issues/3","id":161240652,"number":3,"title":"Rescoring Step","user":{"login":"naimrashid","id":14243418,"avatar_url":"https://avatars.githubusercontent.com/u/14243418?v=3","gravatar_id":"","url":"https://api.github.com/users/naimrashid","html_url":"https://github.com/naimrashid","followers_url":"https://api.github.com/users/naimrashid/followers","following_url":"https://api.github.com/users/naimrashid/following{/other_user}","gists_url":"https://api.github.com/users/naimrashid/gists{/gist_id}","starred_url":"https://api.github.com/users/naimrashid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/naimrashid/subscriptions","organizations_url":"https://api.github.com/users/naimrashid/orgs","repos_url":"https://api.github.com/users/naimrashid/repos","events_url":"https://api.github.com/users/naimrashid/events{/privacy}","received_events_url":"https://api.github.com/users/naimrashid/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-06-20T16:43:36Z","updated_at":"2016-10-04T08:25:41Z","closed_at":"2016-10-04T08:25:41Z","body":"I have read through your TOPPAS code and was wondering at what step the PSM rescoring (as described in the DEMIX publication) is taking place.  The TOPPAS code also uses MSGF-plus, and it is not clear how any filtering is being done post-second pass search.  Is this rescoring still relevant as it is discussed in the publication, or do we now use the scoring based on the MSGF plus scores for filtering?\r\n\r\nWe also had some problems trying to find the IDpicker software to identify and filter protein groups from our output, and instead used peptide/protein prophet (semiparametric model using decoys).  Would this be appropriate in your experience?  Thank you very much for your help"}}
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