I am not sure I understand what you are telling Skyline to do with that XML file.
Bruker raw data is usually in a folder whose name ends in ".d". That folder must contain a file named "analysis.baf" or a file named "analysis.tdf" in order to be recognized by our software as a folder which contains Bruker data.
If you wanted to tell Skyline to extract chromatograms from Bruker raw data, you would use the "File > Import > Results" menu item and point Skyline at the folder whose name ends in ".d".
Which menu item (or commandline command) did you use in Skyline?
What sort of data is in the file "Reference_500ugml_AutoMSMS_T0_33_1_122.xml"?
If you would like to send us files, you can attach small files (less than 50MB) to this support request. You can upload larger files here: