Sam, I believe the spectrum link reads the Comet hits from the Comet produced pep.xml file and generates the Lorikeet spectrum link from that file. Can you confirm you've corrected the mzML path in that file as well?
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/CAJqD6ENToG3o%2BE0Duh8SyW6VOkJtcCHg-q%2B-Y53VW4x7d7f5aQ%40mail.gmail.com.
