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Published 20 hours ago • verified publisher icon compomics

PeptideShaker processing canceled

Open Ysraa opened this issue 3 years ago • 1 comments

Hi,

I am having trouble with certain files not being able to be processed. When I start the search on searchgui it asks to overwrite. Then it gives some errors in the report as you can see in the screenshot attached. I have no idea how to fix this. It works fine with other files.

Best regards! image

Ysraa avatar Jan 03 '22 20:01 Ysraa

Hi! The problem here (at least the one shown in the screenshot) is that MS-GF+ filters out all of the spectra. You can either switch to a different search engine in SearchGUI or change the MS-GF+ settings. If going for the latter, I would recommend having a look at the Fragmentation Method option in the MS-GF+ advanced settings which you can find by clicking the cog while icon to the right of where you select MS-GF+ in the main SearchGUI dialog. Hopefully changing this setting will result in MS-GF+ not filtering out all of your spectra.

hbarsnes avatar Jan 04 '22 10:01 hbarsnes