{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1421","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1421/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1421/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1421/events","html_url":"https://github.com/OpenMS/OpenMS/issues/1421","id":75770442,"number":1421,"title":"QSTAR / wiff data in OpenMS","user":{"login":"oliverschilling","id":8565908,"avatar_url":"https://avatars.githubusercontent.com/u/8565908?v=3","gravatar_id":"","url":"https://api.github.com/users/oliverschilling","html_url":"https://github.com/oliverschilling","followers_url":"https://api.github.com/users/oliverschilling/followers","following_url":"https://api.github.com/users/oliverschilling/following{/other_user}","gists_url":"https://api.github.com/users/oliverschilling/gists{/gist_id}","starred_url":"https://api.github.com/users/oliverschilling/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oliverschilling/subscriptions","organizations_url":"https://api.github.com/users/oliverschilling/orgs","repos_url":"https://api.github.com/users/oliverschilling/repos","events_url":"https://api.github.com/users/oliverschilling/events{/privacy}","received_events_url":"https://api.github.com/users/oliverschilling/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-05-12T22:59:08Z","updated_at":"2015-05-13T09:26:56Z","closed_at":null,"body":"Dear all\r\n\r\nwe are still extensively using a (rather old...) AB/SCiex QSTAR ELITE for a few projects involving tumor tissue analysis. \r\n\r\nIs there any lab with a functional OpenMS peptide ID workflow for QSTAR data (wiff format). Our initial attempts to use OpenMS yielded a 25 % reduction on peptides IDs (5 % FDR) compared to TPP (both using X! Tandem).  \r\n\r\nWe would appreciate any hint / idea / suggestion.  \r\n\r\nThanks\r\n\r\nOliver"},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/101589435","html_url":"https://github.com/OpenMS/OpenMS/issues/1421#issuecomment-101589435","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1421","id":101589435,"user":{"login":"hendrikweisser","id":2251068,"avatar_url":"https://avatars.githubusercontent.com/u/2251068?v=3","gravatar_id":"","url":"https://api.github.com/users/hendrikweisser","html_url":"https://github.com/hendrikweisser","followers_url":"https://api.github.com/users/hendrikweisser/followers","following_url":"https://api.github.com/users/hendrikweisser/following{/other_user}","gists_url":"https://api.github.com/users/hendrikweisser/gists{/gist_id}","starred_url":"https://api.github.com/users/hendrikweisser/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hendrikweisser/subscriptions","organizations_url":"https://api.github.com/users/hendrikweisser/orgs","repos_url":"https://api.github.com/users/hendrikweisser/repos","events_url":"https://api.github.com/users/hendrikweisser/events{/privacy}","received_events_url":"https://api.github.com/users/hendrikweisser/received_events","type":"User","site_admin":false},"created_at":"2015-05-13T09:26:56Z","updated_at":"2015-05-13T09:26:56Z","body":"> A possible explanation is a more conservative vs. less conservative FDR calculation.\r\n\r\nTo test this, could you convert the FDR-filtered (!) TPP results to idXML and apply PeptideIndexer/FalseDiscoveryRate/IDFilter (same FDR threshold) to them? If that removes hits, then our filtering is more aggressive. (This only works if the TPP results still contain decoys.)"}}