Hi Panos You can give it a try with https://github.com/compomics/ThermoRawFileParser . It supports raw -> mgf conversion in Linux, and a raw -> mzML conversion is on the making. I have successfully been able to extract mgf files from RAW files in Linux with this tool. The instructions for how to set it up are given in the README.md file. If you experience difficulties, have a look at the issues (open and closed), or open a new one ;)
Best Antonio lørdag den 2. juni 2018 kl. 21.40.08 UTC+2 skrev Panos Ioannidis: > > 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 >> >> -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
