Issues Loading PRIDE datasets via Reshake

[Zach Flaten]

Hello,

I am getting the following error for what seems like all public datasets 

"PRIDE web server access error. Cannot open: https://www.ebi.ac.uk/pride/ws/archive/assay/list/project/PXD#######"

I have emailed the PRIDE team but I am thinking it as an issue with Peptide Shaker?

Thanks,

-Zach

[Harald Barsnes]

Hi Zach,

I'm afraid it seems like the web service PeptideShaker uses to access the PRIDE data is not available at the moment. Not sure if this is a permanent situation or if it will come back online. However, as indicated in the PRIDE Reshake startup dialog the PRIDE web service was updated almost a year ago and data from after April 2020 is only available via the new PRIDE web service. At some point we hope to get the time to update our code to use the new web service, but at the moment we simply do not have the manpower to look into it. In the meantime you can always find and download the wanted datasets directly from PRIDE (ebi.ac.uk/pride) and process them in SearchGUI/PeptideShaker in a separate step.

Best regards,

Harald