protein FDR filter didn't reach the desired threshold error

[mozzaLB]

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]

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

[AimeeD90]

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

[mozzaLB]

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

[AimeeD90]

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

[mozzaLB]

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

[AimeeD90]

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

[mozzaLB]

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