{"action":"created","issue":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/99","labels_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/99/labels{/name}","comments_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/99/comments","events_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/99/events","html_url":"https://github.com/compomics/peptide-shaker/issues/99","id":119420985,"number":99,"title":"Not recognizing modifications in example dataset - qexactive01819","user":{"login":"EugKapp","id":16076525,"avatar_url":"https://avatars.githubusercontent.com/u/16076525?v=3","gravatar_id":"","url":"https://api.github.com/users/EugKapp","html_url":"https://github.com/EugKapp","followers_url":"https://api.github.com/users/EugKapp/followers","following_url":"https://api.github.com/users/EugKapp/following{/other_user}","gists_url":"https://api.github.com/users/EugKapp/gists{/gist_id}","starred_url":"https://api.github.com/users/EugKapp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/EugKapp/subscriptions","organizations_url":"https://api.github.com/users/EugKapp/orgs","repos_url":"https://api.github.com/users/EugKapp/repos","events_url":"https://api.github.com/users/EugKapp/events{/privacy}","received_events_url":"https://api.github.com/users/EugKapp/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/compomics/peptide-shaker/labels/question","name":"question","color":"cc317c"}],"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":5,"created_at":"2015-11-30T05:28:53Z","updated_at":"2015-12-01T12:26:21Z","closed_at":null,"body":"Hi Guys,\r\n\r\nWe tried loading the example dataset using version 1.1.3 and are concerned by the following: 94.4% unrecognized modifications. We proceeded as follows: Loaded the example dataset, then exported as mzIdentML. Then re-loaded the mzIdentML and specified the mgf, mzId and fasta file (provided in resources/exampledataset/data).\r\n\r\nMon Nov 30 16:16:23 AEDT 2015            - 94.4% unrecognized modifications.\r\nShould we send or attach the report?\r\n\r\nThanks Eugene and Yunshan"},"comment":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/comments/160953693","html_url":"https://github.com/compomics/peptide-shaker/issues/99#issuecomment-160953693","issue_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/99","id":160953693,"user":{"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},"created_at":"2015-12-01T12:26:21Z","updated_at":"2015-12-01T12:26:21Z","body":"Hi Eugene,\r\n\r\nI guess I should know this, but when you refer to \"my own search algorithm\" which algorithm are you then referring to? And regarding adding support for it, would it then be interesting to add it to SearchGUI? This would make it much easier to open the results in PeptideShaker.\r\n\r\nRegarding viewing chimeric spectra, the limitation is currently not so much in PeptideShaker but more in the algorithms supported as none of these support this as far as I know. I know that MS Amanda is working towards it, but nothing is available yet.\r\n\r\nHowever, we do support the annotation of two sets of sequences on the same spectrum in the Spectrum IDs tab. If you select two PSMs for the same spectrum you'll see the information using mirrored spectra. Selecting more than two uses a bubble plot option. (The same is feature is also supported in most other tabs.) Not sure if this was what you were looking for?\r\n\r\nBest regards,\r\nHarald"}}