If you use the new version 1.4 Bruker Compass software, the folder names of routine measurements become a random unique code (GUID) that is not human-readable anymore. OpenChrom now supports opening the Bruker Flex series files, including the vital BioTyper metadata that is inconveniently stored elsewhere. Your data isn’t lost, you just need the right tools to open it.
Bruker Flex Series MALDI-TOF MS file format support including BioTyper metadata
Open Source Spectrometry 