github.com/davidroberson/fragpipe-proteomics-pipeline-tutorial/FragPipe_Convert_Identify_PeptideProphet

The first step of the workflow consists of converting the raw mass spectrometry data to the mzML format using msconvert, followed by the database search using MSFragger, and the peptide validation using PeptideProphet.

MSFragger can only be used for academic research, non-commercial or educational purposes.


This is a companion discussion topic for the original entry at github.com/davidroberson/fragpipe-proteomics-pipeline-tutorial/FragPipe_Convert_Identify_PeptideProphet