{"action":"created","issue":{"url":"https://api.github.com/repos/sneumann/xcms/issues/268","repository_url":"https://api.github.com/repos/sneumann/xcms","labels_url":"https://api.github.com/repos/sneumann/xcms/issues/268/labels{/name}","comments_url":"https://api.github.com/repos/sneumann/xcms/issues/268/comments","events_url":"https://api.github.com/repos/sneumann/xcms/issues/268/events","html_url":"https://github.com/sneumann/xcms/issues/268","id":306405426,"number":268,"title":"Possible addition of centroidization in XCMS","user":{"login":"adelabriere","id":17563377,"avatar_url":"https://avatars0.githubusercontent.com/u/17563377?v=4","gravatar_id":"","url":"https://api.github.com/users/adelabriere","html_url":"https://github.com/adelabriere","followers_url":"https://api.github.com/users/adelabriere/followers","following_url":"https://api.github.com/users/adelabriere/following{/other_user}","gists_url":"https://api.github.com/users/adelabriere/gists{/gist_id}","starred_url":"https://api.github.com/users/adelabriere/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adelabriere/subscriptions","organizations_url":"https://api.github.com/users/adelabriere/orgs","repos_url":"https://api.github.com/users/adelabriere/repos","events_url":"https://api.github.com/users/adelabriere/events{/privacy}","received_events_url":"https://api.github.com/users/adelabriere/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-03-19T10:27:22Z","updated_at":"2018-03-20T11:32:33Z","closed_at":null,"author_association":"NONE","body":"Hello, \r\n\r\nI developped a centroidization algorithm adapted to high resolution MS/MSn which takes as input and xcmRaw object and return a centroided xcmsRaw object. I feel like this could be a good addition to xcms.\r\n\r\nIt was tested on 3 different mass spectrometers TOF, Exactive, Fusion in LC and FIA-MS and worked fine on every use case, with better results than Proteowizard centroidization.\r\n\r\nHowever the algorithm is written in R/C++, and it uses somes Rcpp/C++ features. At the moment it is a simple script which use Rcpp and Inline, and  need to be sourced before every use, therefore there is some work for the transcription in XCMS, especially to write the C++ in C, \r\n\r\nIt may be found here : https://github.com/adelabriere/centroidizationXraw/blob/master/centroidizationScript.R\r\n\r\nIt is quite raw, but it have worked well during my PhD, and it does not require any parameter in the general case, if you are interested I can try to convert it to a cleaner/more adapted form for xcms.\r\n\r\nIn this case some advices will be appreciated about the step to do so will be appreciated, I imagine that I need to define a new S4 method.generic for xcmsRaw and put it there but I have no idea about the rest (Naming/Coding convention etc...)\r\n\r\nThanks,\r\nAlexis\r\n"},"comment":{"url":"https://api.github.com/repos/sneumann/xcms/issues/comments/374565167","html_url":"https://github.com/sneumann/xcms/issues/268#issuecomment-374565167","issue_url":"https://api.github.com/repos/sneumann/xcms/issues/268","id":374565167,"user":{"login":"jotsetung","id":5506112,"avatar_url":"https://avatars3.githubusercontent.com/u/5506112?v=4","gravatar_id":"","url":"https://api.github.com/users/jotsetung","html_url":"https://github.com/jotsetung","followers_url":"https://api.github.com/users/jotsetung/followers","following_url":"https://api.github.com/users/jotsetung/following{/other_user}","gists_url":"https://api.github.com/users/jotsetung/gists{/gist_id}","starred_url":"https://api.github.com/users/jotsetung/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jotsetung/subscriptions","organizations_url":"https://api.github.com/users/jotsetung/orgs","repos_url":"https://api.github.com/users/jotsetung/repos","events_url":"https://api.github.com/users/jotsetung/events{/privacy}","received_events_url":"https://api.github.com/users/jotsetung/received_events","type":"User","site_admin":false},"created_at":"2018-03-20T11:32:33Z","updated_at":"2018-03-20T11:32:33Z","author_association":"COLLABORATOR","body":"> Would be nice to also compare to the vendor centroiding.\r\n\r\nI did that for AB Sciex - they're essentially just reporting the m/z and intensity of the maximum signal. ~ same results as doing a simple `pickPeaks` with the raw, un-smoothed data. Have no other data on hand, so I couldn't check for other manufacturers.\r\n\r\nRegarding *decide on quality of centroiding*: to compare approaches I did:\r\n+ (as @stanstrup suggests above) evaluate accuracy of the centroided data for a set of ~ 60 *known compounds* (difference between theoretical m/z and m/z reported for the identified chromatographic peak).\r\n+ m/z width of the detected chromatographic peaks. I used this as a proxy for the reduction in m/z scattering between consecutive scans, i.e. if the MS detects an ion, the scattering of values around the true m/z should be ideally as low as possible."}}
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