{"action":"created","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1095","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1095/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1095/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1095/events","html_url":"https://github.com/OpenMS/OpenMS/issues/1095","id":50849382,"number":1095,"title":"protein quantification workflows in TPP and OpenMS","user":{"login":"lars20070","id":6149805,"avatar_url":"https://avatars.githubusercontent.com/u/6149805?v=3","gravatar_id":"","url":"https://api.github.com/users/lars20070","html_url":"https://github.com/lars20070","followers_url":"https://api.github.com/users/lars20070/followers","following_url":"https://api.github.com/users/lars20070/following{/other_user}","gists_url":"https://api.github.com/users/lars20070/gists{/gist_id}","starred_url":"https://api.github.com/users/lars20070/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lars20070/subscriptions","organizations_url":"https://api.github.com/users/lars20070/orgs","repos_url":"https://api.github.com/users/lars20070/repos","events_url":"https://api.github.com/users/lars20070/events{/privacy}","received_events_url":"https://api.github.com/users/lars20070/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":108,"created_at":"2014-12-03T15:13:26Z","updated_at":"2015-04-24T08:14:19Z","closed_at":null,"body":"This thread continues the discussion in #1027. As part of the protein inference beta testing, we aim to reproduce roughly the results from a TPP protein quantification published in [1]. Even with a working FidoAdapter, there remain some other issues to be resolved and optimised.\r\n\r\nIn the test dataset, a wild type (wt) mouse skin sample is compared to a Cathepsin L knockout (Ctsl-/-). The two samples were dimethyl labelled heavy (+34Da) and light (+28Da) respectively, mixed and then split into eleven fractions ST366 to ST376.\r\n\r\nThe aim is to roughly re-produce the protein list of the TPP analysis. Many of the high intensity proteins have been checked independently by Western Blotting.\r\n\r\n[1] Tholen et al. CMLS 71(5), 899–916 (Mar. 2014). http://www.ncbi.nlm.nih.gov/pubmed/23233448"},"comment":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/comments/95846214","html_url":"https://github.com/OpenMS/OpenMS/issues/1095#issuecomment-95846214","issue_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1095","id":95846214,"user":{"login":"lars20070","id":6149805,"avatar_url":"https://avatars.githubusercontent.com/u/6149805?v=3","gravatar_id":"","url":"https://api.github.com/users/lars20070","html_url":"https://github.com/lars20070","followers_url":"https://api.github.com/users/lars20070/followers","following_url":"https://api.github.com/users/lars20070/following{/other_user}","gists_url":"https://api.github.com/users/lars20070/gists{/gist_id}","starred_url":"https://api.github.com/users/lars20070/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lars20070/subscriptions","organizations_url":"https://api.github.com/users/lars20070/orgs","repos_url":"https://api.github.com/users/lars20070/repos","events_url":"https://api.github.com/users/lars20070/events{/privacy}","received_events_url":"https://api.github.com/users/lars20070/received_events","type":"User","site_admin":false},"created_at":"2015-04-24T08:14:19Z","updated_at":"2015-04-24T08:14:19Z","body":"Based on three tests, the reported protein scores range from 0 to 0.04 with 70-80% of them 0. The score is not of much use to differentiate between proteins. @jpfeuffer Do you also see this in your Fido tests?\r\n\r\nThe number of peptides for each protein should also appear in the TextExporter output of idXML."}}