I am using MSconvert (Proteowizard) for converting Raw machine data files to mzML format retaining MS2 data. With .RAW (Thermo), I am getting data for MS1 and MS2. For .d (Agilent) files, I get MS1 data only. I have checked raw data on seeMS (ProteoWizard). It is also showing MS1 spectrum for .d files and both specta for .raw files. What must be the issue with .d files? While using msconvert on galaxy, I am facing issue in file selection for .d. please guide me how to fix this issue. Please note that report provided by the vendor for .d files is showing MS2 data. Why I couldn't able to view MS2 data on SEEMS and facing issue in file conversion.