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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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PeptideShaker processing canceled #478

Closed Ysraa closed 1 year ago

Ysraa commented 2 years ago

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

hbarsnes commented 2 years ago

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.