.d file conversion issues in MSConvert

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!

  • When you acquire your datafile in QTOF only mode on your 6560 in masshunter acquisition there should be no particular setting that should potentially impact the downstream file conversion.  If it helps instead and you have masshunter bioconfirm 10- you can export your data file as a MGF and if you have masshunter qualitative 10 you can export as a MGF or mzData.


    As an aside, you did mention chemstation however and I wanted to make sure you meant to refer to masshunter acquisition and you are not referring to the chemstation data file converter as this is meant to convert a chemstation data file to a format that can be read by masshunter qualitative analysis which will not help your current workflow. 

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