ERRO[14:35:10] the protein FDR filter didn't reach the desired threshold, try a higher threshold using the --prot parameter

[DanielConole]

log_2021-11-26_15-20-51.txt

[fcyu]

C:\Users\dconole\Desktop\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.9 --output combined E:\211126-DUB20-mCherry-IP-E3-ligase-target-ID-experiement-3\Fragpipe\filelist_proteinprophet.txt

Is there any reason to set minprob to 0.9? Please note that it is not the threshold for the final result. It controls how many PSMs are used in protein inference. Normally, setting it to 0.7 is good.

Best,

Fengchao

[JensSettelmeier]

log_2022-05-23_10-45-41_protein_FDR_filter_did_not_reach_threshold.txt

Dear Fengchao,

I have the same error message as the original author of #539 (log file attached) and would appreciate your help to solve the error. I checked on the Philosopher github for a parameter called "--prot" to increase as suggested the default threshold (if any set?), but couldn't find a related parameter. Quick details: 0) I followed the tutorial https://fragpipe.nesvilab.org/docs/tutorial_DIA.html

1. I am using the "DIA_DIA-Umprie_SpecLib_Quant" pre-defined workflow with default values.
2. My DIA files in mzML format do not have overlapping windows. I am not sure what is meant with staggered windows though.
3. I used iRT peptides, so I changed the RT calibration option to iRT.
4. Ubuntu 18.04 LTS, 128GB RAM, FragPipe v17.1

I am looking forward to your feedback!

Cheers, jens

[fcyu]

I think it is similar to the other one: https://github.com/Nesvilab/FragPipe/issues/545.

Guo Ci @guoci is this bug fixed?

Thanks,

Fengchao

[guoci]

@fcyu that and this issue probably is not related to the changes I have made to philosopher so far.

[fcyu]

Thanks. Then, I will let Felipe @prvst take a look.

Best,

Fengchao

[prvst]

The log suggests that the peptide validation failed:

Found 0 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 1.78109 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 0 PSMs with q<0.01
Iteration 2:	Estimated 0 PSMs with q<0.01
Iteration 3:	Estimated 0 PSMs with q<0.01
Iteration 4:	Estimated 0 PSMs with q<0.01
Iteration 5:	Estimated 0 PSMs with q<0.01
Iteration 6:	Estimated 0 PSMs with q<0.01
Iteration 7:	Estimated 0 PSMs with q<0.01
Iteration 8:	Estimated 0 PSMs with q<0.01
Iteration 9:	Estimated 0 PSMs with q<0.01
Iteration 10:	Estimated 0 PSMs with q<0.01

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_118_Q2.pep.xml...
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_118_Q3.pep.xml...
...read in 0 1+, 35 2+, 3 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_119_Q1.pep.xml...
...read in 11 1+, 62 2+, 18 3+, 1 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_119_Q2.pep.xml...
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_119_Q3.pep.xml...
...read in 0 1+, 34 2+, 3 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_91_Q1.pep.xml...
...read in 15 1+, 69 2+, 23 3+, 1 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_91_Q2.pep.xml...
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_91_Q3.pep.xml...
...read in 0 1+, 38 2+, 1 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_92_Q1.pep.xml...
...read in 11 1+, 56 2+, 17 3+, 1 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_92_Q2.pep.xml...
...read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Reading in /home/dalco/awesome_proteins/fragepipe_output_B_all_orgas/interact-jsettelmeier_group_B2_92_Q3.pep.xml...
...read in 0 1+, 59 2+, 3 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.7

Please review your parameters, start with the search & validation.