If this is not the first time PEAKS has been installed on your computer, in order to read Agilent raw files in PEAKS, users must first uninstall the 32 bit version of Agilent MassHunter Data Access Component (MHDAC). Then install the 64 bit version either separately or run RegisterMassHunterDataAccess.bat under C:\PEAKSStudio#\MHDAC_x64 directory in Administrator privilege.
How do I load data from my Ion Trap instrument?
Agilent Ion Traps produce a .D folder, which contains all data associated with that data set. The spectral data is contained in the .yep file. CompassXtract can be used to read the .yep file and convert it to an mzXML file inside the .d folder.
CompassXtract is readily available from the Bruker website. It must be installed on the same computer as PEAKS to perform this conversion automatically. Once CompassXtract is installed on your computer, PEAKS will be able to convert Agilent Ion Trap data automatically.