{"action":"created","issue":{"url":"https://api.github.com/repos/compomics/searchgui/issues/80","labels_url":"https://api.github.com/repos/compomics/searchgui/issues/80/labels{/name}","comments_url":"https://api.github.com/repos/compomics/searchgui/issues/80/comments","events_url":"https://api.github.com/repos/compomics/searchgui/issues/80/events","html_url":"https://github.com/compomics/searchgui/issues/80","id":128265864,"number":80,"title":"Peptide Shaker 1.5.0: Import of X! Tandem Results","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/bug","name":"bug","color":"fc2929"}],"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":6,"created_at":"2016-01-22T22:55:48Z","updated_at":"2016-01-23T04:16:31Z","closed_at":null,"body":"Hey folks,\r\n\r\nfirst PS 1.5.0 thingy (a bit following up on the issue #121): after import of my GluC X! Tandem results (which had not worked in 1.4.0) nearly half of my PSMs have a ppm error of <<-20ppm. after closer inspection, it is always peptides with  an N-terminal TMT and at at least TWO fixed modifications (TMT@K or cmCys) present. It seems that as soon as TWO TMT@K are present, the N-terminal TMT is not taken into account anymore.\r\n\r\nPS: I did not rerun my X! Tandem searches in the new SearchGUI. Do I have to?\r\nPPS: In general there is going something wrong with this import, as I end up with 2400 PSMs pointing towards TMT@Nter, whereas Comet, MSGF+, and MsAmanda find only 50-100 (Note: it is a preTAILS sample so is NOT enriched for N-termini)."},"comment":{"url":"https://api.github.com/repos/compomics/searchgui/issues/comments/174132422","html_url":"https://github.com/compomics/searchgui/issues/80#issuecomment-174132422","issue_url":"https://api.github.com/repos/compomics/searchgui/issues/80","id":174132422,"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":"2016-01-23T04:16:31Z","updated_at":"2016-01-23T04:16:31Z","body":"but just a small observation ... I searched with plus/minus 15ppm and now I have 9 hits between plus 15 and 19ppm. so I tried to redo the math, and I guess I use slightly different values than you do, but here my magic math:\r\n\r\nm/z = 631.28313 and the charge 2+   ->   (631.28313*2)-(2*1.007273) = 1260.5517\r\n\r\nthe PSM was identified with an Isotope error of \"1\", thus   -> 1260.5517-1.007273 = 1259.5444\r\n\r\nthe theoretical mass is given as:\r\n1259.52658841083; thus   -> (1259.5444-1259.5266)/(1259.5266)*1000000 = 14.17 ppm\r\n\r\nbut PeptideShaker gives me ***17.25177 ppm***. possible? but maybe my math is just plain wrong."}}