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Rappsilber-Laboratory / xiview

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Not all clickable crosslinks open relevant spectra #556

Closed ciancone94 closed 1 year ago

ciancone94 commented 1 year ago

Hello,

Previously, I have been using XiView (the public website version, xiview.org) to upload XiFDR CSM outputs with corresponding .mgfs and FASTAs with great success; however, recently, when trying to load up spectra corresponding to crosslinks in a photo-leucine crosslinking dataset, many of the spectra will not load. I have not run into this issue with DSSO or SDA crosslinking datasets. I have checked that the relevant .mgfs have been uploaded. Sometimes spectra will load as I click through the PSM IDs and sometimes they won't, with no apparent rhyme or reason as to why. I've ruled out that certain mgfs are the reason as well. Additionally, this seems to be an issue for higher-scored crosslinks; depending on the crosslink, PSMs with lower scores sometimes load a spectrum that won't load for a higher score.

As a caveat, this data is only looking at a purified complex. As there wasn't a lot of linears, I had to boost residue_pairs on XiFDR instead of protein_pairs. Not sure if this matters, but the FDR is quite high.

Thank you,

Anthony

colin-combe commented 1 year ago

Hi Anthony, i think it will be related to these issues; https://github.com/Rappsilber-Laboratory/xiSPEC_spectrumViewer/issues/65 https://github.com/Rappsilber-Laboratory/xiAnnotator/issues/24

we're working on fixing it, i'll keep you posted, Colin

colin-combe commented 1 year ago

for the PSMs that don't display their spectrum, if you open the debugger in the browser (CTRL -SHIFT - J) and look at the console, do you see an error message that starts like: annotation request failed: SyntaxError: Unexpected token

ciancone94 commented 1 year ago

Thanks for the feedback, Colin. When I run the debugger and click on a spectrum that won't load, I get a single instance of the following error:

xiview.org : server does not support RFC 5746, see CVE-2009-3555

Sorry, I see nothing about your predicted error message.

Thanks,

Anthony

colin-combe commented 1 year ago

Hmmm. Maybe the error looks different depending on which browser you're using.

Is it working now or still broken?

Colin

ciancone94 commented 1 year ago

Seems like it's working now, thanks for the fix!