{"action":"created","issue":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/137","repository_url":"https://api.github.com/repos/compomics/peptide-shaker","labels_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/137/labels{/name}","comments_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/137/comments","events_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/137/events","html_url":"https://github.com/compomics/peptide-shaker/issues/137","id":132897821,"number":137,"title":"Phosphosite Localization using PhosphoRS","user":{"login":"wenbostar","id":5302110,"avatar_url":"https://avatars.githubusercontent.com/u/5302110?v=3","gravatar_id":"","url":"https://api.github.com/users/wenbostar","html_url":"https://github.com/wenbostar","followers_url":"https://api.github.com/users/wenbostar/followers","following_url":"https://api.github.com/users/wenbostar/following{/other_user}","gists_url":"https://api.github.com/users/wenbostar/gists{/gist_id}","starred_url":"https://api.github.com/users/wenbostar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wenbostar/subscriptions","organizations_url":"https://api.github.com/users/wenbostar/orgs","repos_url":"https://api.github.com/users/wenbostar/repos","events_url":"https://api.github.com/users/wenbostar/events{/privacy}","received_events_url":"https://api.github.com/users/wenbostar/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/compomics/peptide-shaker/labels/help%20wanted","name":"help wanted","color":"159818"}],"state":"open","locked":false,"assignee":{"login":"mvaudel","id":11632644,"avatar_url":"https://avatars.githubusercontent.com/u/11632644?v=3","gravatar_id":"","url":"https://api.github.com/users/mvaudel","html_url":"https://github.com/mvaudel","followers_url":"https://api.github.com/users/mvaudel/followers","following_url":"https://api.github.com/users/mvaudel/following{/other_user}","gists_url":"https://api.github.com/users/mvaudel/gists{/gist_id}","starred_url":"https://api.github.com/users/mvaudel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvaudel/subscriptions","organizations_url":"https://api.github.com/users/mvaudel/orgs","repos_url":"https://api.github.com/users/mvaudel/repos","events_url":"https://api.github.com/users/mvaudel/events{/privacy}","received_events_url":"https://api.github.com/users/mvaudel/received_events","type":"User","site_admin":false},"milestone":null,"comments":22,"created_at":"2016-02-11T06:00:17Z","updated_at":"2016-02-21T19:34:31Z","closed_at":null,"body":"Hi Harald,\r\nI have tried to use SearchGUI and PeptideShaker to analyze a phosphoproteomic data (http://www.ebi.ac.uk/pride/archive/projects/PXD001792, file:1_QEp2_LC11_SeHu_LivPhos_EarlyInsulin_10s_Bio1.raw).\r\n\r\nBelow is the command line to generate parameter file by using SearchGUI:\r\n\r\n`/home/test/jdk1.8.0_60/jre/bin/java -Djava.awt.headless=true -cp /home/test/SearchGUI-2.6.3.jar eu.isas.searchgui.cmd.IdentificationParametersCLI -out search_new.par -variable_mods \"Phosphorylation of S,Phosphorylation of Y,Phosphorylation of T,Oxidation of M\" -fixed_mods \"Carbamidomethylation of C\" -db mouse_concatenated_target_decoy.fasta -prec_tol 10 -frag_tol 0.05 -max_charge 5 -max_isotope 1 -xtandem_refine 0 -xtandem_evalue 30 -myrimatch_max_pep_length 45 -myrimatch_num_matches 1 -myrimatch_num_ptms 3 -myrimatch_fragmentation cid -comet_num_matches 1 -comet_max_frag_charge 5 -useGeneMapping 0 -updateGeneMapping 0 -annotation_level 0.98 -import_peptide_length_min 7 -import_peptide_length_max 45 -ptm_score 1 -score_neutral_losses 0 -db_pi mouse_concatenated_target_decoy.fasta -psm_fdr 0.01 -peptide_fdr 0.01 -protein_fdr 0.01 -msgf_instrument 3 -msgf_fragmentation 3 -msgf_protocol 1 -msgf_min_pep_length 7 -msgf_max_pep_length 45 -msgf_num_matches 1 -msgf_additional 1 -msgf_termini 2 -msgf_num_ptms 3\r\n`\r\n\r\nBelow is the command line of PeptideShaker \r\n\r\n`java -Xmx60G -cp  /home/test/PeptideShaker-1.7.4.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment phos -sample phos -replicate 1 -identification_files /home/test/searchgui_3se_result/searchgui_out.zip -out  /home/test/my_3se.cpsx -spectrum_files /home/test/phos1.mgf -id_params /home/test/search_new.par -temp_folder /home/test/tmmmp`\r\n\r\nHowever, the result of phosphosite scoring is weird. Below is the PSM report file:\r\n[phos_phos_1_Default_PSM_Report.txt.tar.gz](https://github.com/compomics/peptide-shaker/files/125938/phos_phos_1_Default_PSM_Report.txt.tar.gz)\r\n\r\n\r\nCould you please take a look at this file?\r\n\r\nBest regards!\r\nBo"},"comment":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/comments/186895627","html_url":"https://github.com/compomics/peptide-shaker/issues/137#issuecomment-186895627","issue_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/137","id":186895627,"user":{"login":"mvaudel","id":11632644,"avatar_url":"https://avatars.githubusercontent.com/u/11632644?v=3","gravatar_id":"","url":"https://api.github.com/users/mvaudel","html_url":"https://github.com/mvaudel","followers_url":"https://api.github.com/users/mvaudel/followers","following_url":"https://api.github.com/users/mvaudel/following{/other_user}","gists_url":"https://api.github.com/users/mvaudel/gists{/gist_id}","starred_url":"https://api.github.com/users/mvaudel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvaudel/subscriptions","organizations_url":"https://api.github.com/users/mvaudel/orgs","repos_url":"https://api.github.com/users/mvaudel/repos","events_url":"https://api.github.com/users/mvaudel/events{/privacy}","received_events_url":"https://api.github.com/users/mvaudel/received_events","type":"User","site_admin":false},"created_at":"2016-02-21T19:34:31Z","updated_at":"2016-02-21T19:34:31Z","body":"Hi Bo,\n\nThank you for the testing. This is a rounding issue in the cumulative\nprobability estimation. I will try to find a way around this problem\ntomorrow.\n\nBest regards,\n\nMarc\n\n2016-02-21 6:07 GMT+01:00 wenbostar <notifications@github.com>:\n\n> Hi Marc,\n> Thank you very much. I have tested the new version (1.8.0-beta), however\n> it didn't work. Below is the error message:\n>\n> Sun Feb 21 12:56:33 CST 2016 Computing PSM probabilities.\n> 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\n> Sun Feb 21 12:56:33 CST 2016 Scoring PTMs in PSMs (D-score and PhosphoRS)\n> Sun Feb 21 12:56:33 CST 2016 Scoring PSM PTMs. Please Wait...\n> java.lang.IllegalArgumentException: PhosphoRS probability > 1.\n> at\n> com.compomics.util.experiment.identification.ptm.ptmscores.PhosphoRS.getSequenceProbabilities(PhosphoRS.java:248)\n> at\n> eu.isas.peptideshaker.ptm.PtmScorer.attachProbabilisticScore(PtmScorer.java:320)\n> at eu.isas.peptideshaker.ptm.PtmScorer.scorePTMs(PtmScorer.java:419)\n> at\n> eu.isas.peptideshaker.ptm.PtmScorer$PsmPtmScorerRunnable.run(PtmScorer.java:2373)\n> at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)\n> at java.util.concurrent.FutureTask.run(FutureTask.java:266)\n> at\n> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\n> at\n> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\n> at java.lang.Thread.run(Thread.java:745)\n>\n> Best regards!\n> Bo\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/compomics/peptide-shaker/issues/137#issuecomment-186746835>\n> .\n>\n"}}