{"action":"created","issue":{"url":"https://api.github.com/repos/compomics/searchgui/issues/85","labels_url":"https://api.github.com/repos/compomics/searchgui/issues/85/labels{/name}","comments_url":"https://api.github.com/repos/compomics/searchgui/issues/85/comments","events_url":"https://api.github.com/repos/compomics/searchgui/issues/85/events","html_url":"https://github.com/compomics/searchgui/issues/85","id":129337399,"number":85,"title":"MSGF+","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/help%20wanted","name":"help wanted","color":"159818"}],"state":"open","locked":false,"assignee":{"login":"hbarsnes","id":13151214,"avatar_url":"https://avatars.githubusercontent.com/u/13151214?v=3","gravatar_id":"","url":"https://api.github.com/users/hbarsnes","html_url":"https://github.com/hbarsnes","followers_url":"https://api.github.com/users/hbarsnes/followers","following_url":"https://api.github.com/users/hbarsnes/following{/other_user}","gists_url":"https://api.github.com/users/hbarsnes/gists{/gist_id}","starred_url":"https://api.github.com/users/hbarsnes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hbarsnes/subscriptions","organizations_url":"https://api.github.com/users/hbarsnes/orgs","repos_url":"https://api.github.com/users/hbarsnes/repos","events_url":"https://api.github.com/users/hbarsnes/events{/privacy}","received_events_url":"https://api.github.com/users/hbarsnes/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2016-01-28T04:54:35Z","updated_at":"2016-01-28T18:29:43Z","closed_at":null,"body":"Hey folks,\r\n\r\nhaving some issues with MSGF+, mainly its rather low ID rate compared to the others (X!Ta, Ms Amanda, Comet). So in my test data sets from today around 10% instead of 20% in the others. thus i started to test the \"advanced\" settings again, and interestingly, this time some made no difference at all and gave me exactly the same file size at the end and the exact same PSMs after PeptideShaker.\r\n\r\nSo I varied e.g. the instrument setting, which handles as far as I understand it also MS2 accuracy. Tested three of them, TOF, LTQ, and Orbi - but all gave the exact same result. Then I checked CID vs HCD, and again, exactly the same.\r\n\r\nwhen I did this kind of testing the last time, they all made a difference. but maybe there is also something \"special\" with these data. just wondering if something is going wrong, especially as my ID rate is currently rather low - especially for LysR and GluC, and especially for the latter it frequently outperformed the others (but with data form an other instrument, so that could be also a reason).\r\n\r\ncan you look into that? would be great.\r\n\r\nPS: I checked of course the SearchGUI report, and at least officially my settings were all set. so e.g. this:\r\n\r\n***Search Parameters:***\r\n- \tPrecursorMassTolerance: 10.0ppm\r\n- \tIsotopeError: 0,1\r\n- \tTargetDecoyAnalysis: false\r\n- \t***FragmentationMethod: HCD***\r\n- \t***Instrument: QExactive***\r\n- \tEnzyme: Semi-LysargiNase\r\n- \tProtocol: TMT\r\n- \tNumTolerableTermini: 1\r\n- \tMinPeptideLength: 7\r\n- \tMaxPeptideLength: 35\r\n- \tNumMatchesPerSpec: 3\r\n\r\ngave exactly the same result as:\r\n\r\n***Search Parameters:***\r\n\r\n- \tPrecursorMassTolerance: 10.0ppm\r\n- \tIsotopeError: 0,1\r\n- \tTargetDecoyAnalysis: false\r\n- \t***FragmentationMethod: CID***\r\n- \t***Instrument: TOF***\r\n- \tEnzyme: Semi-LysargiNase\r\n- \tProtocol: TMT\r\n- \tNumTolerableTermini: 1\r\n- \tMinPeptideLength: 7\r\n- \tMaxPeptideLength: 35\r\n- \tNumMatchesPerSpec: 3"},"comment":{"url":"https://api.github.com/repos/compomics/searchgui/issues/comments/176324672","html_url":"https://github.com/compomics/searchgui/issues/85#issuecomment-176324672","issue_url":"https://api.github.com/repos/compomics/searchgui/issues/85","id":176324672,"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":"2016-01-28T18:29:43Z","updated_at":"2016-01-28T18:29:43Z","body":"hmm ... good to know ... it is just that MSGF+ performs really poorly right now on LysR and GluC data, but does reasonable well with ArgC data. but didn't find a real pattern yet.\r\n\r\nI somehow think I may just find too many decoys, as my ID rate for MSGF+ goes significantly up when importing the results from Comet, MSGF+, MsAmanda and X!Tandem at the same time.\r\n\r\nwhat would be the best way to test that via SearchGUI - exporting all PSMs? so also the unvalidated ones and decoy ones and check/compare there?\r\n\r\nin the past MSGF+ alsways performed great on our data, but these were on Orbitrap instruments (XL, Velos, QExact) and not on the Impact II."}}