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protein FDR filter didn't reach the desired threshold error

Open mozzaLB opened this issue 1 year ago • 7 comments

log_2024-08-28_17-03-46.txt

I found some old closed issues describing the same problem but there is no solution offered. I am also running into this protein FDR issue using Fragpipe V22 and was wondering if there is already a solution to this issue? Please see log file attached

mozzaLB avatar Aug 29 '24 10:08 mozzaLB

Surprisingly, if I take a subset of the LCMS files as input, there is no FDR error, even when using 14 out of the 16 files initially

mozzaLB avatar Aug 30 '24 09:08 mozzaLB

Can you share those .pep.xml files from 1_Burg_ctrl_H2O_1 folder? That will help us locate the error.

AimeeD90 avatar Oct 01 '24 20:10 AimeeD90

1_Burg_ctrl_H2O_1.zip Sorry for the delayed response. Please find attached the pepXML files from the folder you mentioned.

mozzaLB avatar Oct 11 '24 08:10 mozzaLB

Thanks, but could you please share the interact-*.pep.xml files instead?

AimeeD90 avatar Oct 11 '24 15:10 AimeeD90

There is only one interact-*.pep.xml file interact.pep.xml.zip

mozzaLB avatar Oct 11 '24 17:10 mozzaLB

Can you share the combined.prot.xml file as well? Looks like too many decoy proteins there

AimeeD90 avatar Oct 12 '24 14:10 AimeeD90

There is no combined.prot.xml file in this folder or the main folder. Where can I find it?

mozzaLB avatar Oct 14 '24 07:10 mozzaLB