No output of peptide with low score in validation model

[YongchaoDou]

psm.txt

Using the same mgf file, there are only scores output for the first and second peptides.

#######command line
java -jar pepquery-2.0.2/pepquery-2.0.2.jar -ms 20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.mgf -db refseq:human -hc -o pepquery_out/ -i psm.txt -s 2 -indexType 2 -minScore 0

#######PSM file

FHWEQDQIAHMK 20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.100019.100019.2 File:"20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.raw", NativeID:"controllerType=0 controllerNumber=1 scan=100019"
MQKEITALAPSTMK 20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.100022.100022.3 File:"20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.raw", NativeID:"controllerType=0 controllerNumber=1 scan=100022"
FWEQDQIAHK 20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.100019.100019.2 File:"20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.raw", NativeID:"controllerType=0 controllerNumber=1 scan=100019"
MKEITALAPSTK 20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.100022.100022.3 File:"20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.raw", NativeID:"controllerType=0 controllerNumber=1 scan=100022"

#######output file
peptide modification n spectrum_title charge exp_mass tol_ppm tol_da isotope_error pep_mass mz score n_db total_db n_random total_random pvalue
MQKEITALAPSTMK - 1 20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.100022.100022.3 File:"20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.raw", NativeID:"controllerType=0 controllerNumber=1 scan=100022" 3 1547.810664502653 -3.5719342021607288 -0.005528658103003181 0.0 1547.80513584455 516.944164634363 25.129905651418486 0 220 0 10 0.09090909090909091
FHWEQDQIAHMK - 1 20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.100019.100019.2 File:"20190601_QX6_JoMu_SA_uPac200cm_HeLa_f5.raw", NativeID:"controllerType=0 controllerNumber=1 scan=100019" 2 1568.7209883368062 -0.9920589585905434 -0.001556262166104716 0.0 1568.71943207464 785.367770635215 27.235389558263975 0 126 0 10 0.09090909090909091

[wenbostar]

Could you share the parameter setting you used for your fragpipe search? You will need to make sure your PepQuery parameter setting matches well with the setting you used to generate the PSMs.

[YongchaoDou]

fragger.params.txt

This is the parameter file of fraggerPipe

[wenbostar]

I believe you will be able to get scores for all your PSMs if you make sure the following settings are consistent between the two tools:

Fixed modification
Variable modification
MS1 mass tolerance
MS2 mass tolerance
Isotope error setting
Enzyme setting
The number of missed cleavage sites

[YongchaoDou]

I will give it a try.