PepXML > spectrum > top hits viewer issue - Comet

[Sam Whedon]

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

[Luis Mendoza]

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

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[Jimmy Eng]

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 <whed...@gmail.com> wrote:

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[Sam Whedon]

Hi all,

Thanks for the helpful suggestions. Fortunately, if the filepath for the mzML data is incorrect I get an error screen that specifies the current incorrect filepath in the xml.

It turns out that I omitted an important detail. This error was arising after processing the pep.xml with Libra through xinteract.

When I edit the URL for comparing the top hits from "File=C%3A%2F...my_data.mzML.gz..." to "File=C%3A%2F...my_data.mzML..." it works despite my data being in mzML.gz format.

If I edit the original pep.xml file so that raw_data=".mzML" then I can view the top hits.

I never converted my data from mzML.gz to mzML, so I see an error message on the page listing the top comet hits:

Error - cannot read spectrum (mzML) file C:/my_data.mzML -- links to spectra may not work

But the all of the annotate msms spectra show up and look fine in Lorikeet. 

Apologies for the long read.

Thanks again for your help.

Best,

Sam 

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