Thermo Orbitrap RAW files to mzML for DDA label-free proteomics

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Hello,

I am trying to convert Thermo Orbitrap RAW files to mzML for DDA label-free proteomics analysis on usegalaxy.eu.

My original RAW file (20261002_F_SN3842.raw, approximately 1.85 GB) uploaded successfully.

However, I have encountered two problems:

  1. Thermo RAW File Converter (version 1.3.4+galaxy1): The job has remained in the new state for over 12 hours without starting.

  2. msconvert (version 3.0.26121.8): The conversion failed with exit code 255. The Galaxy error report does not provide additional diagnostic details.

Could you please investigate whether these are server-side issues and advise which tool is currently recommended for converting Thermo RAW files to mzML?

Thank you for your assistance.