--decoys doesn't work for the DIA data

[nitz1bug]

Hi,

I have been using FragPipe to analyze some DIA data and I need decoys to appear in the 'psm.tsv' output file but I haven't been able to figure out how to get this to work. I have been able to get this information for my DDA data, but not for my DIA data.

I have run both the DIA_SpecLib_Quant workflow and the DIA_DIA-Umpire_SpecLib_Quant workflow. For each workflow, I made the following changes to the defaults for the workflow before running the analysis:

• checked 'Print decoys' on the 'Validation - FDR Filter and Report' pane
• unchecked 'Generate spectral library from search results' on the 'Spec Lib - Spectral library generation' pane
• added a spectral library file to the 'Quant (DIA) - FDR' pane

Additionally, some of my testing to try and get decoy information has included adding the following flags to the 'Validation - FDR Filter and Report' pane:
--prot 1.0
--psm 1.0
--ion 1.0
--pep 1.0
--pepProb 0
--protProb 0

I would appreciate any help you could provide!

Thanks!

[fcyu]

Thank for the bug reporting. I have confirmed that it is a bug in Philosopher. Let me transfer it.

Best,

Fengchao