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 <mark.athana...@gmail.com> 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 <scienceg...@gmail.com> > 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 < >> spctools-discuss@googlegroups.com> 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 <scienceg...@gmail.com> 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 spctools-discuss+unsubscr...@googlegroups.com. >>>> 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 spctools-discuss+unsubscr...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. >> 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 spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAL-xMntU9ysQP_vCqGOWfu91z8-r7j2RmwWerjCHSTG1ZBA8XA%40mail.gmail.com.
