Yes, I did think of setting up a Windows VM for such conversions, and maybe 
it's unavoidable after all...

Thanks a lot for your time!

P

On Saturday, 2 June 2018 19:06:48 UTC+3, Michael Hoopmann wrote:
>
> No, there isn't a native tool for Linux that reads vendor formats. 
> Unfortunately, vendor formats are proprietary and requires the vendor 
> drivers to access those files and convert them. All of those drivers are 
> Windows only, as the vendors have decided that is their platform of choice. 
> Thermo will eventually release a Linux compatible driver set for Mono, 
> maybe you can even get your hands on the development version - but it will 
> only read the file. Converting it to another format will require additional 
> coding or interfacing with ProteoWizard.
>
> One possible solution would be to create a Windows virtual machine for 
> converting vendor formats. It can be fired up inside Linux, then convert 
> the vendor files to mzML using msconvert from ProteoWizard, copy the mzML 
> files back to your Linux filesystem, and wind down the VM.
>
> Cheers,
> Mike
>
>

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