If you follow the link further https://skyline.ms/wiki/home/software/Skyline/page.view?name=OverlappingWindowScheme&_docid=wiki%3A41195689-d578-1036-894e-e465a393d561
they explain how to actually make the isolation scheme in skyline that is compatible with several MS manufacturers; I believe the file is quite large. You may need to re-acquire your data under these circumstances. On Thu, Oct 22, 2020 at 5:08 PM Science Gurl <[email protected]> wrote: > Hi Mark, > > Thanks for the suggestion... This is what I've been doing but I get an > error. I'll switch this query to the SkyLine team for some more > troubleshooting! > -jane > > On Thu, 22 Oct 2020 at 17:04, Mark Athanason <[email protected]> > wrote: > >> Jane, >> >> See this from the Skyline team: >> >> https://skyline.ms/wiki/home/software/Skyline/page.view?name=DemultiplexingOverlappingDIAWindows >> >> Best >> Mark >> >> On Thu, Oct 22, 2020 at 4:28 PM Science Gurl <[email protected]> >> wrote: >> >>> Hey David! >>> >>> Yes, I'd like to know more about DISCo. I was poking around that tool >>> too and kinda got lost :) That's what 3 years away from proteomics will do >>> for you! The MSconvert within TPP creates mzML files fine, I guess I don't >>> know how to check to see if they have been demultiplexed. Can I use them >>> in DISCo or should I use the MS2 fragment extractor? >>> >>> -JN >>> >>> On Thu, 22 Oct 2020 at 16:17, 'David Shteynberg' via spctools-discuss < >>> [email protected]> wrote: >>> >>>> Dear Jane, >>>> >>>> I cannot help you with the demultiplexing, because I have not used that >>>> feature before in MSConvert. But if you do manage to get a regular DIA >>>> mzML file out of the conversion you can use the DISCo tool available in the >>>> TPP under Tools->DIA->Extract MS2 Fragments that will generate a new mzML >>>> file that you can search and analyze with DDA tools. As DISCo has recently >>>> seen major improvements I can provide you with a release candidate version >>>> if you are interested. >>>> >>>> Cheers, >>>> -David >>>> >>>> On Thu, Oct 22, 2020 at 1:08 PM jane n <[email protected]> wrote: >>>> >>>>> Hi all, >>>>> >>>>> I have acquired a bunch of files on my Eclipse to build a DIA library >>>>> using an 8mz window in overlap mode (ie essentially 4mz windows) and I'm >>>>> not clear if the Convert to MzML is demultiplexing to 4mz windows? I've >>>>> tried doing it manually in MSconvert but the conversion fails. On the >>>>> other hand, do I need to demulitplex? >>>>> >>>>> Cheers! >>>>> -Jane >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/spctools-discuss/af9c2037-59d0-478e-bcfc-d0d09adabd29n%40googlegroups.com >>>>> <https://groups.google.com/d/msgid/spctools-discuss/af9c2037-59d0-478e-bcfc-d0d09adabd29n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D97cbNtG3XjUbopu-seY-rU4bj8peX-UG1cL948Tgi17g%40mail.gmail.com >>>> <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D97cbNtG3XjUbopu-seY-rU4bj8peX-UG1cL948Tgi17g%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/spctools-discuss/CAL-xMntWrAeuTJqOL69rOZf3wRJO2hOmvUuthThmSo6d4ag7cw%40mail.gmail.com >>> <https://groups.google.com/d/msgid/spctools-discuss/CAL-xMntWrAeuTJqOL69rOZf3wRJO2hOmvUuthThmSo6d4ag7cw%40mail.gmail.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/CABW2DNrj4nbxyaTYa9NBxoFfM0wYq1xOOczLvJ5T70RgYaEZfw%40mail.gmail.com >> <https://groups.google.com/d/msgid/spctools-discuss/CABW2DNrj4nbxyaTYa9NBxoFfM0wYq1xOOczLvJ5T70RgYaEZfw%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CAL-xMntU9ysQP_vCqGOWfu91z8-r7j2RmwWerjCHSTG1ZBA8XA%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CAL-xMntU9ysQP_vCqGOWfu91z8-r7j2RmwWerjCHSTG1ZBA8XA%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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