Open search on non-Tryptic peptides

[WrennPockTwo]

Dear FragPipe team, thanks a lot for creating and maintaining this wonderful tool for mass spectrometry!

My problem is based on the open search. I am used to get unmodified peptides as the major hit in my open search under normal (tryptic) conditions. However, an open search using lysn_promisc as the enzyme does not yield any unmodified peptides. Is this expected or to I use the workflow incorrectly.

Thanks a lot for any help here Best regards, Max

I attached the lysn_promisc open search log file: log_2024-01-16_12-31-15.zip and the corresponding output log_2024-01-16_12-31-15.zip log_2024-01-16_12-31-15_ptm-shepherd-output.zip

I attached the trypsin open search log file: log_2024-01-04_13-06-20.zip and the corresponding output log_2024-01-04_13-06-20.zip log_2024-01-04_13-06-20_ptm-shepherd-output.zip