Re: [spctools-discuss] PepXML > spectrum > top hits viewer issue - Comet

[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


On Mon, Feb 19, 2024 at 10:16 PM Jimmy Eng  wrote:

> 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  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
>>
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>> 
>> .
>>
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Re: [spctools-discuss] PepXML > spectrum > top hits viewer issue - Comet

[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  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
>
> --
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> 
> .
>

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Re: [spctools-discuss] PepXML > spectrum > top hits viewer issue - Comet

['Luis Mendoza' via spctools-discuss]

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  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.
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> 
> .
>

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