How do I load data from my Bruker instrument?
Bruker instruments produce a .D folder, which contains all data associated with that data set. The spectral data is contained in the .yep, or .baf file or in the .lift folder. CompassXtract can be used to read the 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 Bruker data automatically.
You can load and merge .lift files into a single data file by selecting the directory level one above the group of .lift files when loading the data into PEAKS. In PEAKS, under Preferences -> Bruker, be sure that you have selected ‘yes’ to ‘Bruker .fid file may contain several files, do you want to merge them?’