Intensity = 0 in the combined_protein.tsv and combined_peptide.tsv

[Sarah-Lennon]

Dear all,

I have recently downloaded MSFragger 16.0 and upgraded to MSFragger-3.3.jar and philospher 4.0.0.
I have processed 4 files and all my intensities are 0 in the combined_protein.tsv and combined_peptide.tsv. I am not sure why.
combined_protein.txt

I did the same processing with MSFragger 15.0, MSFragger-3.2.jar and philosopher 3.4.13 and did not encounter this issue.
combined_protein.txt

Please find enclosed:

• the log file for MS fragger 15
  log_2021-09-21_09-42-29.txt
• the config file for MSFragger.15
  Fragpipe_MSFragger15.txt
• The log file for MSFragger 16
  Uploading log_2021-09-17_17-28-51.txt…
• the config file for MSFragger 16
  Fragpipe_16.txt

Thank you very much for your help !

Sarah

[Fengchao]

Hi Sarah,

The key information, the log file for MSFragger 16, is not included in your message. Could you please send us the log?

Thanks,

Fengchao

[Sarah-Lennon]

oh yes sorry for that. Here we go
log_2021-09-17_17-28-51.txt
Thank you very much !
Sarah

[Fengchao]

Hi Sarah,

This is a known bug (Nesvilab/FragPipe#420 (comment)). The solution for now is unchecking print decoys in FDR filter and report panel. It is unchecked by default, could you tell us the reason of checking this box?

Best,

Fengchao

[Sarah-Lennon]

Hi Fengchao,

Thank you very much for your fast answer ! I have just tried and indeed it has worked.
No particular reason to leave the decoys, I checked the box, the first time I used MsFragger to have a closer look at the results and kept it on since. I imported my method from MSFragger 15.0.

Thank you again,

Sarah

[Fengchao]

You are welcome.

Best,

Fengchao