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As part of the CPGR's hands-on tutorial in proteomics, I trained the students on the use of database search engines to identify proteins for comparative proteomics experiments. In this video I demonstrate the use of the FragPipe GUI to launch MSFragger in a typical "narrow" search. The pepXMLs that we created could then be interpreted through IDPicker to produce a spectral count table. Through MSFragger did not require us to change data format from RAW to mzML or MGF, I also showed the use of ProteoWizard msConvertGUI. The data we employed came from the ABRF iPRG 2009 "red" vs. "yellow" E. coli challenge.