Discrepancy between MSFragger config and params used by MSFragger

[bltsai-UCLA]

Hello,

I noticed that some of the parameters listed in the pepXML output from MSFragger don't match with the parameters listed in my input config file. The expected parameters in the config file are:

• fragment_mass_tolerance = 25
• deisotope = 1
• deneutralloss = true

But the parameters listed in the pepXML are:

• fragment_mass_tolerance = 300
• deisotope = 0
• deneutralloss = false

MSFragger config file:
fragger.params.txt

Configs from pepXML:
pepXML.txt

Thanks in advance!

[prvst]

Hi @bltsai-UCLA That is a known issue that got fixed a while ago. The fix will be present in the next release. For now, try running MSFragger before running the pipeline command.