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.
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