Hi Sam, It does sound like potentially an issue with the mzML file path(s) inside the comet pepXML results, though there could be other issues.
As for troubleshooting, you can inspect the URL of those troublesome links and look for the Dta= (or File=) parameter -- is the filepath the same that you expect on the local drive? You can also compare that to one of the links that do work to look for differences, as sometimes they might be subtle -- e.g. a missing slash etc. Hope this helps, --Luis On Mon, Feb 19, 2024 at 7:41 PM Sam Whedon <whedo...@gmail.com> wrote: > Hi all, > > I am using the Pep.XML viewer with Comet data in the Comet pipeline. If I > click a link in the ions column Lorikeet produces an annotated spectrum as > anticipated. If I click on the spectrum link in the same row, navigating to > a page showing comet hits, then none of the spectrum viewer links work > (individual links in the 'ions' column or the lower 'view and compare top > hits'). The comet hits window shows multiple top hits, and correctly > annotates the ion count for each hit. > I am running comet on a cluster, then downloading the pep.xml, and > correcting the mzML and fasta filepaths in the xml text before viewing in > the trans proteomic pipeline. > Please let me know if there is anything I can try to troubleshoot this > problem. > Thanks. > > Best, > Sam > > -- > 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/95845bc2-c844-4bcc-8d7f-a1b34eb54bb7n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/95845bc2-c844-4bcc-8d7f-a1b34eb54bb7n%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/CACyS9boQeTNKWw%2BXgRXuLd1zjzTPT3fAkSmGptqpRFrV8G-0-Q%40mail.gmail.com.
