- updated MSFragger version to 4.1 and Crux version to 4.2

ProteoWizard / pwiz

The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.

http://proteowizard.sourceforge.net/

Apache License 2.0

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Closed chambm closed 1 week ago

chambm commented 2 weeks ago

added most advanced MSFragger params to the "Additional Options" dialog
changed Percolator to run on all MSFragger pepXML files together to get experiment-level q-values
changed pepXML "fixing" code to insert Percolator scores into the MSFragger pepXML (because the new Crux version doesn't write a pepXML)

chambm commented 1 week ago

@brendanx67 Should this be cherry picked to release?