I'm a new user to the Agilent 6560 ion mobility Q-TOF at my university. I am using the Q-TOF in non-ion mobility mode in DDA to acquire proteomics data. The .d files generated are not converting to mzml files for use in downstream proteomic analysis. Are there particular settings in Chemstation that I need to apply when generating my file that are not obvious? I'm not sure if it is my .d file that is the issue or the MSConvert software.
Thank you for any help!