{"action":"closed","issue":{"url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1850","repository_url":"https://api.github.com/repos/OpenMS/OpenMS","labels_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1850/labels{/name}","comments_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1850/comments","events_url":"https://api.github.com/repos/OpenMS/OpenMS/issues/1850/events","html_url":"https://github.com/OpenMS/OpenMS/issues/1850","id":137212927,"number":1850,"title":"spectra from mobility mzml files cannot be extracted when the experiments involve selection/fragmentation","user":{"login":"lopippo","id":16020903,"avatar_url":"https://avatars.githubusercontent.com/u/16020903?v=3","gravatar_id":"","url":"https://api.github.com/users/lopippo","html_url":"https://github.com/lopippo","followers_url":"https://api.github.com/users/lopippo/followers","following_url":"https://api.github.com/users/lopippo/following{/other_user}","gists_url":"https://api.github.com/users/lopippo/gists{/gist_id}","starred_url":"https://api.github.com/users/lopippo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lopippo/subscriptions","organizations_url":"https://api.github.com/users/lopippo/orgs","repos_url":"https://api.github.com/users/lopippo/repos","events_url":"https://api.github.com/users/lopippo/events{/privacy}","received_events_url":"https://api.github.com/users/lopippo/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/OpenMS/OpenMS/labels/File%20Format","name":"File Format","color":"fbca04"},{"url":"https://api.github.com/repos/OpenMS/OpenMS/labels/OpenMS%20-%20library","name":"OpenMS - library","color":"207de5"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-02-29T10:29:55Z","updated_at":"2016-04-19T20:01:48Z","closed_at":"2016-04-19T20:01:48Z","body":"Greetings, \r\n\r\nI am having trouble iterating into an OnDiscMSExperiment<> instance when that is instance\r\nloads an mzML file that contains mobility data (Waters Synapt 2) from an experiment that involves ion selection/fragmentation either before or after the mobility separation. Interestingly, I can get the number of spectra fine, even if the iteration in  then fails. (See code below)\r\n\r\nMobility experiments can be loaded and parsed fine as long as they do not involve precursor ions selection. \r\n```\r\n // Load data from an indexed MzML file\r\n OnDiscMSExperiment<> ondmseMap;\r\n imzml.load(globalOptions.mzmlFilename(), ondmseMap);\r\n\r\n QString dateTimeString = expSettings->getDateTime().getDate().toQString();\r\n(works fine)\r\n\r\n /* the number of spectra in this whole mzml file */\r\n uint numberOfSpectra = ondmseMap.getNrSpectra();\r\n specMetaData.setIntItem(\"spectrumListCount\", numberOfSpectra);\r\n(works fine)\r\n\r\n for(uint specIndex = 0; specIndex < numberOfSpectra; ++specIndex)\r\n {\r\n  MSSpectrum<> spectrum = ondmseMap.getSpectrum(specIndex);\r\n(crashes)\r\n```\r\n\r\nOpenMS version 2.0.0 gotten from GitHub dated 20160120.\r\n\r\nHow can I help ? I could provide the three files where I see the crash:\r\n\r\n- simple quadrupole selection -> mobility -> time-of-flight\r\n- quadrupole selection -> fragmentation -> mobility -> time-of-flight\r\n- quadrupole selection -> mobility -> fragmentation -> time-of-flight\r\n\r\nOnly roughly 6-7 Mb each.\r\n\r\nSincerely,\r\nFilippo Rusconi\r\nDebian packager of OpenMS (but here with my scientist hat on)"}}